Class: Bioroebe::Shell

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/shell/menu.rb,
lib/bioroebe/shell/shell.rb,
lib/bioroebe/shell/readline.rb,
lib/bioroebe/shell/help/class.rb

Overview

Bioroebe::Shell

Defined Under Namespace

Classes: Help

Constant Summary collapse

TRUNCATE_AT_N_ELEMENTS =
#

TRUNCATE_AT_N_ELEMENTS

If we display nucleotide strings, then by default, these may be very long. So the following constant will act as a threshold.

#
2000
SHALL_WE_DEBUG =
#

SHALL_WE_DEBUG

#
false
RUBY_SRC = 
"#{HOME_DIRECTORY_OF_USER_X}programming/ruby/src/"
BIOROEBE = 
ENV['HOME']
FILE_USE_SILENT_STARTUP =
#

FILE_USE_SILENT_STARTUP

#
"#{::Bioroebe.project_base_directory?}shell/configuration/use_silent_startup.yml"
MAIN_EDITOR =

else assume that we may be on windows.

'notepad++.exe'
MY_EDITOR =

MY_EDITOR

MAIN_EDITOR
BIOSHELL_SAVE_FILE = 
'/home/Temp/bioroebe/shell_file.md'
HOME_DIR =

This is valid at home.

home_dir+'.gem/gems/bioroebe-'+
Bioroebe.version?.to_s+'/lib/bioroebe/'
DEFAULT_PADDING =
#

DEFAULT_PADDING

#
'  '
COMPLETION_PROC =
#

COMPLETION_PROC

#
proc { |s|
  (ARRAY_WITH_COMPLETIONS.grep(/^#{Regexp.escape(s.to_s)}/)+
  self.return_entries_in_the_current_directory.map {|entry|
    (entry+'/').squeeze('/')
  }).flatten
}

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from CommandlineApplication

#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codons_for?, #colourize_this_dna_sequence, #cp, #disable_warnings, #download_dir?, #editor?, #enable_warnings, #ensure_that_the_base_directories_exist, #esystem, #extract, #is_this_a_start_codon?, #is_this_a_stop_codon?, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opnerev, #opnn, #pad_with_double_quotes, #pad_with_single_quotes, #partner_nucleotide, #remove_numbers, #remove_trailing_ansii_escape_code, #return_all_possible_start_codons, #return_array_of_one_letter_aminoacids, #return_cheerful_person, #return_chunked_display, #return_ubiquitin_sequence, #runmode?, #set_be_verbose, #set_runmode, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into

Methods included from BaseModule

#absolute_path, #default_file_read, #file_readlines

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens, #set_commandline_arguments

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods inherited from Base

#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #is_on_roebe?, #main_encoding?, #mkdir, #move_file, #mv, #no_file_exists_at, #project_yaml_directory?, #rds, #register_sigint, #return_the_first_line_of_this_file, #word_wrap, #write_what_into

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

Methods included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Constructor Details

#initialize(commandline_arguments = ARGV, run_already = true) ⇒ Shell

#

initialize

#


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# File 'lib/bioroebe/shell/shell.rb', line 186

def initialize(
    commandline_arguments = ARGV,
    run_already           = true
  )
  reset # Must come first, to create @internal_hash.
  set_commandline_arguments(
    commandline_arguments
  )
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :do_not_run_yet
    # ===================================================================== #
    when :do_not_run_yet
      run_already = false
    end
  end
  # ======================================================================= #
  # Intercept some important commandline arguments next. This must come
  # AFTER we invoked set_commandline_arguments().
  # ======================================================================= #
  case first?
  # ======================================================================= #
  # === no_colours
  #
  # This variant is different from the variant in menu() in that another
  # method will be called to disable the colours.
  #
  # Invocation example:
  #
  #   biosh --disable-colours
  #
  # ======================================================================= #
  when 'nocol',
       'noco',
       /^-?-?no(_|-| )?colou?rs?$/,
       /^-?-?disable(_|-| )?colours$/,
       'dcolours'
    disable_colours_in_an_extended_manner(:be_quiet)
  # ======================================================================= #
  # === bioroebe --help
  #
  # This entry-point will quickly show which options are available for
  # the bioshell.
  # ======================================================================= #
  when /^-?-?help$/
    show_commandline_options
  # ======================================================================= #
  # === bioshell --controller
  # ======================================================================= #
  when /^-?-?controller$/i
    require 'bioroebe/gui/gtk3/controller/controller.rb'
    ::Bioroebe.run_gtk_controller
    exit_program
  # ======================================================================= #
  # === bioshell --do-not-create-directories-on-startup
  # === bioshell --do-not-create-directories
  #
  # Do not create directories on startup.
  #
  # Invocation example:
  #
  #   bioshell --do-not-create-directories-on-startup
  #
  # ======================================================================= #
  when /^-?-?do(-|_| )?not(-|_| )?create(-|_| )?directories(-|_| )?on(-|_| )?startup$/i,
       /^-?-?do(-|_| )?not(-|_| )?create(-|_| )?directories$/i
    @internal_hash[:create_directories_on_startup_of_the_shell] = false
  # ======================================================================= #
  # === bioroebe --protein-to-dna
  #
  # This entry point will try to start the ruby-gtk3 protein-to-DNA
  # converting widget.
  # ======================================================================= #
  when /^-?-?protein(-|_| )?to(-|_| )?dna$/i
    require 'bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb'
    ::Bioroebe::GUI::Gtk::ProteinToDNA.run_gtk3_widget
    exit
  # ======================================================================= #
  # === bioshell --permanently-disable-startup-intro
  # === bioshell --permanently-disable-startup-notice
  # === bioshell --permanently-no-startup-intro
  # === bioshell --permanently-no-startup-info
  # ======================================================================= #
  when /^-?-?permanently(-|_)?disable(-|_)?startup(-|_)?intro$/,
       /^-?-?permanently(-|_)?disable(-|_)?startup(-|_)?notice$/,
       /^-?-?permanently(-|_)?no(-|_)?startup(-|_)?intro$/,
       /^-?-?permanently(-|_)?no(-|_)?startup(-|_)?info$/
    permanently_disable_startup_intro
  # ======================================================================= #
  # === :no_commandline_arguments
  # ======================================================================= #
  when :no_commandline_arguments
    # ===================================================================== #
    # Simply pass through in this case.
    # ===================================================================== #
  # ======================================================================= #
  # === :exit_gracefully
  # ======================================================================= #
  when :exit_gracefully
    set_exit_gracefully
  # ======================================================================= #
  # === bioroebe --silent-startup
  # ======================================================================= #
  when /^-?-?silent(-|_)?startup$/,
       /^-?-?silent$/
    do_a_silent_startup
  # ======================================================================= #
  # === bioroebe --random-aminoacids=33
  # === bioroebe --n-aminoacids=33
  # ======================================================================= #
  when /^-?-?random(-|_)?aminoacids=(.+)$/i,
       /^-?-?n(-|_)?aminoacids=(.+)$/i
    n_aminoacids = $2.to_s.dup
    ::Bioroebe.create_random_aminoacids(n_aminoacids) { :do_report }
    exit
  # ======================================================================= #
  # === bioroebe --rnafold=cdna.MT.fa
  # ======================================================================= #
  when /^-?-?rnafold=(.+)$/
    try_to_run_rnalfold_on_this_file($1.to_s.dup)
    exit
  # ======================================================================= #
  # === bioroebe --fasta=/Depot/Bioroebe/Arabidopsis_thaliana_chromosome_5_sequence.fasta
  # ======================================================================= #
  when /^-?-?fasta=(.+)$/
    this_fasta_file = $1.to_s.dup
    if File.exist?
      handle_fasta(this_fasta_file)
    else
      e 'No file could be found at `'+sfile(this_fasta_file)+'`.'
    end
  # ======================================================================= #
  # === bioroebe --n-fasta-entries
  #
  # Usage example:
  #
  #   cd /root/Bioroebe/Downloads/; bioroebe --n-fasta-entries
  #
  # ======================================================================= #
  when /^-?-?n(-|_)?fasta(-|_)?entries$/
    require 'bioroebe/fasta/display_how_many_fasta_entries_are_in_this_directory.rb'
    ::Bioroebe::DisplayHowManyFastaEntriesAreInThisDirectory.new
    exit
  # ======================================================================= #
  # === bioroebe --split-this-fasta-file-into-chromosomes=Mus_musculus.GRCm38.ncrna.fa
  # ======================================================================= #
  when /^-?-?split(-|_)?this(-|_)?fasta(-|_)?file(-|_)?into(-|_)?chromosomes=(.+)$/i # $6
    _ = $6.to_s.dup
    require 'bioroebe/fasta/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb'
    ::Bioroebe::SplitThisFastaFileIntoChromosomes.new(_)
    exit
  # ======================================================================= #
  # === bioroebe --stats
  #
  # This entry-point will show some simple fasta-statistics, from
  # the current directory.
  #
  # Usage example:
  #
  #   cd /root/Bioroebe/Downloads/; bioroebe --stats
  #
  # ======================================================================= #
  when /^-?-?stats$/i,
       /^-?-?statistics$/i,
       /^-?-?fasta(-|_)?stats$/i
    require 'bioroebe/fasta/show_fasta_statistics.rb'
    ::Bioroebe.show_fasta_statistics(Dir['*'])
    exit
  # ======================================================================= #
  # === bioroebe --download=ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
  #
  # This entry point allows us to download a remote program.
  #
  # Invocation example:
  #
  #   bioroebe --download=ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
  #   bioroebe --download ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
  #
  # Note that the second variant currently (April 2020) does not work -
  # let's see if we need it again in the future.
  # ======================================================================= #
  when /^-?-?download=(.+)/
    ::Bioroebe.download($1.to_s.dup)
  # ======================================================================= #
  # === bioroebe --sequence=150
  #
  # This entry point allows us to use any sequence, on startup.
  #
  # Invocation example:
  #
  #   bioroebe --sequence=1505
  #
  # ======================================================================= #
  when /^-?-?sequence (.+)/,
       /^-?-?sequence=(.+)/
    set_dna($1.to_s.dup, :be_quiet) # Be quiet here when doing the assignment.
  # ======================================================================= #
  # === bioroebe --show-exon-statistics-for=/tmp/praktikum/Mouse/chromosome_8/parsed/cdna.8.L100.global.gtf
  # ======================================================================= #
  when /^-?-?show(-|_)?exon(-|_)?statistics(-|_)?for=(.+)$/ # === $4
    ::Bioroebe.show_exon_statistics($4.to_s.dup)
    exit
  # ======================================================================= #
  # === bioroebe --sinatra
  # ======================================================================= #
  when /^-?-?sinatra$/i
    do_start_the_sinatra_interface
    return
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::Shell[]

#


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# File 'lib/bioroebe/shell/shell.rb', line 11902

def self.[](i = ARGV)
  new(i)
end

.colour? ⇒ Boolean

#

Bioroebe::Shell.colour?

Query-method over @default_colour.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 140

def self.colour?
  @default_colour
end

.generate_pdf_tutorial(also_upload_the_tutorial = true) ⇒ Object

#

Bioroebe::Shell.generate_pdf_tutorial

You can use this method to simply generate a new .pdf file, then upload it anyway.

#


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# File 'lib/bioroebe/shell/shell.rb', line 11850

def self.generate_pdf_tutorial(
    also_upload_the_tutorial = true
  )
  url = ::Bioroebe.try_to_pass_through_beautiful_url('bioroebe_tutorial?pdf')
  url = url.first if url.is_a? Array
  url.gsub!(/^\/home\/x\/data\//, LOCALHOST) if url.include? HOME_DIRECTORY_OF_USER_X+'data/'
  OpenURI.send(:open, url)
  # ======================================================================= #
  # === Designate where the tutorial can be found locally
  # ======================================================================= #
  path = FILE_BIOROEBE_TUTORIAL
  if also_upload_the_tutorial
    if File.exist? path
      ::Bioroebe.upload_this_pdf_file(path)
    else
      e "Can not upload from #{sfile(path.to_s)} as this "\
        "path does not exist."
    end
  end
end

.menu(i = ARGV) ⇒ Object

#

Bioroebe::Shell.menu

To test this, try:

Bioroebe::Shell.menu('ll')
#


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# File 'lib/bioroebe/shell/shell.rb', line 11840

def self.menu(i = ARGV)
  new(:no_commandline_arguments).menu(i)
end

.return_entries_in_the_current_directory ⇒ Object

#

Bioroebe::Shell.return_entries_in_the_current_directory

#


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# File 'lib/bioroebe/shell/readline.rb', line 46

def self.return_entries_in_the_current_directory
  Dir['*']
end

.set_colour(i) ⇒ Object

#

Bioroebe::Shell.set_colour

Set the default colour here.

#


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# File 'lib/bioroebe/shell/shell.rb', line 157

def self.set_colour(i)
  @default_colour = i
end

.upload_this_pdf_file(path) ⇒ Object

#

Bioroebe::Shell.upload_this_pdf_file

Use this method to upload the .pdf tutorial or any other .pdf file. This is primarily useful on my home system and may have very little value to other people.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1892

def self.upload_this_pdf_file(path)
  # ======================================================================= #
  # ^^^ This will have generated the .pdf.
  # ======================================================================= #
  # Hardcoded for now where the .pdf will reside.
  # ======================================================================= #
  if Object.const_defined? :FtpParadise
    ftp = FtpParadise.new(:shevy, :dont_run_yet)
    ftp.
    ftp.upload_this_binary_file(path)
    e 'Finished uploading!'
  end
end

Instance Method Details

#aa_to_dna(i) ⇒ Object

#

aa_to_dna

#


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# File 'lib/bioroebe/shell/shell.rb', line 10774

def aa_to_dna(i)
  if i.is_a? Array
    i = i.join.strip
  end
  i = ::Bioroebe.aa_to_dna(i)
  if i.is_a? Array
    i = i.join.strip
  end
  e i
end

#add_his_tag(i = 'add 6 random his tags') ⇒ Object

#

add_his_tag

This method can be used to add a his tag. By default we will add 6 Histidin tags in succession. This pattern is commonly found in expression vectors.

These histidin tags will be randomly placed within the DNA sequence, by default. Note that CAT and CAC code for Histidin. In most vectors, there is an alternation between these codons.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8987

def add_his_tag(
    i = 'add 6 random his tags'
  )
  n_his_tags_to_add = i.scan(/\d+/).first
  position = rand(main_sequence?.size)+1
  e 'Next adding '+sfancy(n_his_tags_to_add)+rev+
    ' Histidin tags to our main sequence at nucleotide '\
    'position '+sfancy(position.to_s)+rev+'.'
  _ = main_sequence?
  _.insert_at_this_position(
    position+1, 'CAC|CAT|CAC|CAT|CAC|CAT' # Insert the His tag here.
  )
  assign_this_dna_sequence(_.to_str)
end

#add_n_nucleotides ⇒ Object

#

add_to_start

Use this method to add to the start of a nucleotide sequence. In other words, to prepend to the main nucleotide sequence.

#

add_n_nucleotides



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# File 'lib/bioroebe/shell/shell.rb', line 6922

def add_to_start(i)
  add_to_start_or_end(i, :to_start)
end

#add_poly_a_sequence ⇒ Object

#

add_poly_a_sequence

Use this method to tag a PolyA sequence to the 3’ end of a mRNA.

First, the mRNA will be cleaved by the enzyme CPSF, usually at the sequence AAUAAA (most common one, but variants exist). AAUAAA is found in 90% of all sequenced polyadenylation elements.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5660

def add_poly_a_sequence
  this_sequence = 'A' * 250
  @internal_hash[:rna].append(this_sequence)
end

#add_the_current_user_input_to_the_history ⇒ Object

#

add_the_current_user_input_to_the_history

#


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# File 'lib/bioroebe/shell/shell.rb', line 4901

def add_the_current_user_input_to_the_history
  # ======================================================================= #
  # And add the user-input to the array that keeps track of it. This
  # has to be done through a specific method, which can do additional
  # checks before adding the user-input onto the history.
  # ======================================================================= #
  add_to_history(user_input?)
end

#add_timer_snapshot ⇒ Object

#

add_timer_snapshot

#


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# File 'lib/bioroebe/shell/shell.rb', line 8915

def add_timer_snapshot
  array_timer_snapshots? << Time.now
end

#add_to_end(i) ⇒ Object Also known as: add

#

add_to_end

This method will invoke append() if something has to be appended.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6027

def add_to_end(i)
  add_to_start_or_end(i, :end)
end

#add_to_history(i = user_input? ) ⇒ Object Also known as: append_this_onto_the_history

#

add_to_history

This method should be used consistently whenever content is added onto the history of the bioshell. Content in this context refers primarily to user-submitted input.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7322

def add_to_history(
    i = user_input?
  )
  if i.is_a? Array
    i.each {|entry| add_to_history(entry) }
  else
    i = i.to_s.chomp
    unless i.empty?
      if array_history? and array_history?.respond_to?(:last)
        last_history_element = array_history?.last # <- On startup there is no history, hence this check as safeguard.
        if last_history_element
          unless (last_history_element.strip == i.strip) # Only add if it is new input.
            array_history? << i
            if log_user_input?
              what = "#{i}#{N}"
              into = "#{bioshell_log_dir?}input_history.yml"
              append_what_into(what, into)
            end
          end
        else # This clause is valid for new entries.
          array_history? << i
        end
      end
    end
  end
end

#add_to_start(i) ⇒ Object Also known as: left_add

#

add_to_start

#


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# File 'lib/bioroebe/shell/shell.rb', line 6920

def add_to_start(i)
  add_to_start_or_end(i, :to_start)
end

#add_to_start_or_end(i = '', append_or_prepend = :append) ⇒ Object

#

add_to_start_or_end

This method can either add to the start or to the end.

The default is to append to the nucleotide sequence.

We can input a number - in this case, we simply add these many nucleotides onto the main string.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10311

def add_to_start_or_end(
    i                 = '',
    append_or_prepend = :append
  )
  if the_main_sequence_is_frozen?
    report_that_the_main_sequence_is_frozen
    return
  end
  i = i.join('') if i.is_a? Array
  i = i.dup
  old_length = i.size
  case i.to_s # Easier start/stop entries.
  # ======================================================================= #
  # === Add a start codon.
  # ======================================================================= #
  when 'start',
       'START',
       /ORF/i,
       ':start'
    i = ::Bioroebe.start_codon? # Used to be hardcoded -> 'ATG'
  # ======================================================================= #
  # === Add a stop codon.
  # ======================================================================= #
  when /^stop$/i,
       ':stop'
    i = ::Bioroebe.stop_codons?.sample
  end
  i = i.dup if i.frozen?
  i.upcase!
  case append_or_prepend
  # ======================================================================= #
  # === :prepend
  # ======================================================================= #
  when :prepend,
       :to_start,
       :start
    if i =~ /^\d+$/ # If input is only numbers.
      erev 'Only numbers were given: Prepending '+
            sfancy(i.to_s)+rev+
           ' random nucleotides to the main string now.'
      i.to_i.times { prepend(add_nucleotide) }
    else
      erev "Prepending #{sfancy(i)}#{rev} to the main string."
      prepend(i)
    end
  # ======================================================================= #
  # === :append
  # ======================================================================= #
  when :append,
       :to_end,
       :end
    if i =~ /^\d+$/ # If input is only numbers.
      erev "Only numbers were given: Adding #{sfancy(i.to_s)}#{rev}"\
           " random nucleotides to the main string now."
      i.to_i.times { append(return_random_nucleotide) }
    else
      if only_nucleotides?(i)
        msg = "Adding #{sfancy(i)}#{rev}"
        msg = msg.dup if msg.frozen?
        if ::Bioroebe.is_a_stop_codon? i
          msg << ' (a stop codon)'
        end
        msg << ' to the main string.'
        erev msg
      end
      append(i)
    end
  end
  new_length = string?.size.to_s
  unless new_length.to_i == old_length.to_i
    erev "The new length of the main string is now: "\
         "#{simp(new_length)}#{rev}."
  end
  show_dna_sequence
end

#add_vertical_barrier_to_sequence(i = dna_sequence? ) ⇒ Object

#

add_vertical_barrier_to_sequence

This will turn a sequence such as “ATGCCC” into “ATG|CCC”.

Invocation example:

barrier ATGCCC
#


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# File 'lib/bioroebe/shell/shell.rb', line 10957

def add_vertical_barrier_to_sequence(
    i = dna_sequence?
  )
  i = i.join if i.is_a? Array
  i = dna_sequence? if i.nil?
  splitted = i.scan(/.../)
  joined = splitted.join('|')
  e joined
end

#adenin? ⇒ Boolean

#

adenin?

This will return e. g. “C5H5N5”.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8318

def adenin?
  YAML.load_file(FILE_NUCLEOTIDES)['Adenin']
end

#align_ORFS(i = dna_string? ) ⇒ Object

#

align_ORFS

This method is used to align all intrinsic ORFs of agiven sequence.

We delegate into class AlignOpenReadingFrames for the output.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2136

def align_ORFS(
    i = dna_string?
  )
  i = dna_string? if i.nil?
  ::Bioroebe::AlignOpenReadingFrames.new(i) # bl $BIOROEBE/align_open_reading_frames.rb
end

#all_arguments? ⇒ Boolean Also known as: a?

#

all_arguments? (a? tag)

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7446

def all_arguments?
  @internal_hash[:all_arguments]
end

#all_upcase?(i) ⇒ Boolean Also known as: is_all_upcase?

#

all_upcase?

Return true if the input is all upcased.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6751

def all_upcase?(i)
  return true if i.upcase == i
  return false
end

#analyze(i = sequence? ) ⇒ Object

#

analyze (analyze tag)

The input to this method should be the DNA or aminoacid sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6693

def analyze(
    i = sequence?
  )
  if i.is_a? Array
    i << sequence? if i.empty?
    i = i.join
  end
  # ======================================================================= #
  # We require a String past this point.
  # ======================================================================= #
  i = i.to_s
  if File.exist? i # Assume that we have a .pdb file here for now.
    parse_this_pdb_file(i)
  else
    if block_given?
      yielded = yield
      case yielded
      when :dna # Handle DNA "input" here.
        analyze_dna_string(i)
      else
        do_analyze_sequence(i)
      end
    else # Default case without block.
      do_analyze_sequence(i)
    end
  end
end

#analyze_dna_string(i = dna_string? ) ⇒ Object

#

analyze_dna_string

This method presently only counts the amount of nucleotides found in the given DNA string at hand.

We use the class Bioroebe::CountAmountOfNucleotides, in bl count_amount_of_nucleotides.rb

#


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# File 'lib/bioroebe/shell/shell.rb', line 8138

def analyze_dna_string(
    i = dna_string?
  )
  # ======================================================================= #
  # Set some default values:
  # ======================================================================= #
  i = dna_string? if i.nil?
  if i.is_a? Array and i.empty?
    i = dna_string?
  end
  ::Bioroebe::CountAmountOfNucleotides.new(
    i, :use_cliner
  ) {{ use_colours: use_colours? }} # bl $BIOROEBE/count_amount_of_nucleotides.rb
end

#annotate_this_file(i) ⇒ Object

#

annotate_this_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 9293

def annotate_this_file(i)
  ::Bioroebe::CreateAnnotationFormat.new(i)
end

#append(i) ⇒ Object

#

append (append tag)

You can use this to simply append to the main string.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3388

def append(i)
  i = i.join.strip if i.is_a? Array
  i = i.to_s
  # ======================================================================= #
  # First check whether the main sequence is frozen:
  # ======================================================================= #
  if is_the_main_sequence_frozen?
    report_that_the_main_sequence_is_frozen
  else
    case i # case tag
    # ===================================================================== #
    # === start
    # ===================================================================== #
    when 'start'
      i = ::Bioroebe.start_codon?
      erev 'We will append the START codon '+sfancy(i)+rev+' next.'
    # ===================================================================== #
    # === stop
    #
    # Add a random stop-codon in this case.
    # ===================================================================== #
    when 'stop'
      i = ::Bioroebe.stop_codons?.sample
      erev 'We will append the STOP codon '+sfancy(i)+rev+' next.'
    when 'shine'
      i = 'AGGAGGT' # Can only add nucleotides to the main sequence.
      erev 'We will append the '+mediumslateblue('Shine Dalgarno')+
           rev+' (SD) sequence '+sfancy("#{i}-3")+rev+' next.'
    end
    if i =~ /^\d+$/ # If input is only numbers.
        erev "Only numbers were given: Adding #{sfancy(i.to_s)}#{rev}"\
             " random nucleotides to the main string next."
      new_string = ''.dup
      i.to_i.times { new_string << return_random_nucleotide }
      i = new_string
    end
    # ===================================================================== #
    # === Check that we add only DNA or RNA nucleotides past this point
    # ===================================================================== #
    if only_nucleotides?(i)
      erev "Now appending #{simp(i)}#{rev}."
      sequence_object? << i # Next, append to the sequence object here.
      show_DNA_sequence
    else
      # ===================================================================== #
      # The user may also wish to append a restriction site, such
      # as via add EcoRI. We need to enable this here.
      # ===================================================================== #
      _ = ::Bioroebe.return_sequence_that_is_cut_via_restriction_enzyme(i, :no_colours)
      if _
        _.tr!('|','')
        erev "Now appending #{simp(_)}#{rev}."
        sequence_object? << _ # Next, append to the sequence object here.
        show_dna_sequence
      else
        erev 'Can not add the sequence '+simp(i)+rev+' because there '\
             'are non-nucleotides in it.'
      end
    end
  end
end

#array_fasta? ⇒ Boolean

#

array_fasta?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 9953

def array_fasta?
  @internal_hash[:array_fasta]
end

#array_history? ⇒ Boolean

#

array_history?

Access the input-history of the bioshell.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 5145

def array_history?
  @internal_hash[:array_history]
end

#array_timer_snapshots? ⇒ Boolean

#

array_timer_snapshots?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8922

def array_timer_snapshots?
  @internal_hash[:array_timer_snapshots]
end

#assign_sequence2(i) ⇒ Object

#

assign_sequence2

#


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# File 'lib/bioroebe/shell/shell.rb', line 7468

def assign_sequence2(i)
  i = i.join(' ') if i.is_a? Array
  @internal_hash[:sequence2] = Bioroebe::Sequence.new(i)
end

#assume_what_type_this_is(i) ⇒ Object

#

assume_what_type_this_is

Determine what type the given input is.

Note that this currently has limitations in that it does not use a statistical way to determine whether we really have DNA/RNA/Aminoacids here.

Eventually we will write a replacement for it but for now, it has to suffice.

To test this method interactively, do this in the shell:

assume ATCG
assume AUCG
assume NNNLMMLLAAA
#


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# File 'lib/bioroebe/shell/shell.rb', line 7232

def assume_what_type_this_is(i)
  if i.is_a? Array
    i = i.join
  end
  if i
    chars = i.chars
    if    chars.all? {|entry| POSSIBLE_DNA_NUCLEOTIDES.include? entry }
      erev 'This must be a DNA sequence.'
    elsif chars.all? {|entry| POSSIBLE_RNA_NUCLEOTIDES.include? entry }
      erev 'This must be a RNA sequence.'
    elsif chars.all? {|entry| POSSIBLE_AMINO_ACIDS.include? entry }
      erev 'This must be an amino acid sequence.'
    else
      erev 'This can not be a valid sequence ('+
            simp('DNA/RNA/Proteins')+rev+').'
    end
  else
    erev 'Missing an input such as '+sfancy('ATCG')+rev+'.'
  end
end

#attempt_to_discover_dna_A_boxes ⇒ Object

#

attempt_to_discover_dna_A_boxes

#


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# File 'lib/bioroebe/shell/shell.rb', line 7081

def attempt_to_discover_dna_A_boxes
  dna_A_box_sequence = 'TTATCCACA'
  erev 'The dnaA box in E. coli has this consensus sequence:'
  e
  efancy "  #{dna_A_box_sequence}#{rev}"
  e
  unless string?.empty?
    results = string?.scan(/#{dna_A_box_sequence}/)
    if results.empty?
      erev 'The given DNA sequence does not contain any dnaA sequence elements.'
    else
      erev 'This sequence can be found '+simp(results.size.to_s)+rev+' times.'
      pp results
    end
  end if dna_sequence?
end

#automatically_rename_this_fasta_file(i) ⇒ Object

#

automatically_rename_this_fasta_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 6818

def automatically_rename_this_fasta_file(i)
  [i].flatten.compact.each {|this_fasta_file|
    Bioroebe.automatically_rename_this_fasta_file(this_fasta_file)
  }
end

#backtranseq(i = aminoacid_sequence?, , output_as_dna_or_rna = :dna) ⇒ Object Also known as: translate_aminoacids_into_dna

#

backtranseq

Translate an Aminoacid Sequence back into the most likely DNA sequence that would code for this sequence/protein. Thus, this method translates from Aminoacids to DNA sequence - in other words it does a “reverse-lookup”.

Currently, we hardcode to the homo sapiens frequency codon table, but at a later time, we will probably change to a more flexible layout, to allow a backtranseq for more organisms.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4965

def backtranseq(
    i                    = aminoacid_sequence?,
    output_as_dna_or_rna = :dna
  )
  sequence = ConvertAminoacidToDNA[i].to_str.delete('-')
  erev lpad?+
       leading_five_prime+
       sfancy(sequence)+
       rev+
       trailing_three_prime
  erev 'Note that we have also assigned the above to be the new DNA sequence.'
  assign_sequence(sequence, :be_silent)
end

#bioshell_log_dir? ⇒ Boolean

#

bioshell_log_dir?

This method will return where the bioshell/ log dir is kept.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 9720

def bioshell_log_dir?
  "#{log_dir?}bioshell/"
end

#bisulfite(i) ⇒ Object

#

bisulfite

#


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# File 'lib/bioroebe/shell/shell.rb', line 5709

def bisulfite(i)
  return ::Bioroebe.bisulfite_treatment(i)
end

#calculate_atp_cost_for(i = aminoacid_sequence?) ) ⇒ Object

#

calculate_atp_cost_for

This method can be used to calculate the ATP cost in order to synthesize a protein.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7259

def calculate_atp_cost_for(i = aminoacid_sequence?)
  i = i.join.strip if i.is_a? Array
  if i.nil?
    i = aminoacid_sequence?
  end
end

#calculate_exponential_growth(a, b) ⇒ Object

#

calculate_exponential_growth

#


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# File 'lib/bioroebe/shell/shell.rb', line 6445

def calculate_exponential_growth(a, b)
  erev ::Bioroebe.calculate_exponential_growth(a,b)
end

#calculate_hamming_distance_of(i) ⇒ Object

#

calculate_hamming_distance_of

We will delegate into class HammingDistance here.

The argument to this method should ideally be an Array.

To test this method, do:

hamming AGUUCGAUGG AGUCCGGUCG
hamming AGUUCGAUGGGGGGGTTT AGUCCGGUCGGGG
random 100; setseq2 hamming 1 2
#


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# File 'lib/bioroebe/shell/shell.rb', line 5847

def calculate_hamming_distance_of(i)
  if i.is_a? String
    if i.include? ' ' and i =~ /^\d+/ # The String could be "1 3" here, for instance.
      splitted = i.split(' ').map(&:strip)
      case splitted.size
      when 2 # If we have at least 2 entries.
        splitted[-1] = return_sequence_from_this_number(splitted[-1])
        splitted[0]  = return_sequence_from_this_number(splitted[0])
        i = splitted.join(' ')
      end
    end
  end
  ::Bioroebe::HammingDistance[i] # bl $BIOROEBE/hamming*rb
end

#calculate_melting_temperature(i) ⇒ Object

#

calculate_melting_temperature

This method just delegates towards class CalculateMeltungTemperature.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6000

def calculate_melting_temperature(i)
  i = string? if i.nil?
  if i == :show_formulas
    CalculateMeltingTemperature.show_formulas # bl $BIOROEBE/calculate_melting_temperature.rb
  else
    @_.calculate_melting_temperature(i)
  end
end

#calculate_time_difference ⇒ Object

#

calculate_time_difference

#


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# File 'lib/bioroebe/shell/shell.rb', line 8929

def calculate_time_difference
  (@internal_hash[:array_timer_snapshots][-2] - @internal_hash[:array_timer_snapshots][-1]) 
end

#calculcate_at_content(i = dna_sequence? ) ⇒ Object

#

calculcate_at_content

Calculate the AT content of a DNA or RNA sequence.

Usage examples:

set_dna ATGCGCGCGCGAACGATGCATGACTGCTAGTCGACA; calc_at_content
calc_at_content AAAGGG
#


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# File 'lib/bioroebe/shell/shell.rb', line 738

def calculcate_at_content(
    i = dna_sequence?
  )
  if i.is_a? Array
    i = i.first
  end
  i = dna_sequence? if i.nil?
  i.upcase!
  total = i.size
  n_A = i.count('A')
  n_T = i.count('T')
  result = ( (n_A + n_T) * 100 ) / total
  erev 'The AT content of this sequence is '+
        simp(result.to_s)+rev+' %.'
end

#calculcate_gc_content(i = dna_sequence_as_string? ) ⇒ Object

#

calculcate_gc_content

Use this method to calculate the GC content of a DNA sequence.

If you need the number, you can use this piece of code:

CalculateGCContent.gc_percentage(i) # Will return the percentage number.
#


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# File 'lib/bioroebe/shell/shell.rb', line 943

def calculcate_gc_content(
    i = dna_sequence_as_string?
  )
  if i.nil? or i.empty? # The second check also checks for empty Arrays.
    i = dna_sequence_as_string? # bl $BIOROEBE/calculate/calculate_gc_content.rb
  end
  CalculateGCContent.new(i)
end

#change_first_nucleotide_to(i = dna_sequence? ) ⇒ Object

#

change_first_nucleotide_to

This will only work if we had already assigned a DNA sequence prior to running it.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5599

def change_first_nucleotide_to(
    i = dna_sequence?
  )
  i = i.join(' ').strip if i.is_a? Array
  unless i.empty?
    i = i.upcase
    erev "Now changing the first nucleotide to `#{simp(i)}`."
    sequence?.first_nucleotide = i
    show_string
  end
end

#chdir(i = :default) ⇒ Object Also known as: cd

#

chdir (cd tag)

#


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# File 'lib/bioroebe/shell/shell.rb', line 9995

def chdir(
    i = :default
  )
  if i and i.start_with?('cd ')
    i[0,3] = ''
  end
  case i
  # ======================================================================= #
  # === :home
  # ======================================================================= #
  when :home,
       ':home'
    i = log_dir?
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default,
       nil
    i = File.expand_path('~').to_s
  end
  if File.directory? i
    ::Bioroebe.change_directory(i)
  else
    e "No directory at #{sdir(File.absolute_path(i))}#{rev} "\
      "appears to exist."
  end
end

#check_for_local_vectors ⇒ Object

#

check_for_local_vectors

#


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# File 'lib/bioroebe/shell/shell.rb', line 3067

def check_for_local_vectors
  _ = return_available_vectors
  unless _.empty? # Silent assignment comes next.
    set_sequence_2(::Bioroebe::Sequence.sequence_from_file(_.first))
  end
end

#check_for_mismatches ⇒ Object

#

check_for_mismatches

#


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# File 'lib/bioroebe/shell/shell.rb', line 5206

def check_for_mismatches
  CheckForMismatches.new
end

#chop(i = 1, chop_from_left_or_right_hand_side = :default) ⇒ Object Also known as: remove_n_nucleotides

#

chop (chop tag)

We use this method to get rid of some nucleotides, from the 3’ end of a nucleotide sequence (aka the “right hand side” of it) by default.

The first argument to this method tells us how many nucleotides are to be removed.

The second argument determines whether to chop from the right side (the 3’ side) or from the left side (the 5’ side).

#


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# File 'lib/bioroebe/shell/shell.rb', line 10400

def chop(
    i = 1,
    chop_from_left_or_right_hand_side = :default # The default is the 3' end.
  ) # Default will be to chop off one nucleotide.
  if is_the_main_sequence_frozen?
    report_that_the_main_sequence_is_frozen
    return
  end
  i = i.first if i.is_a? Array
  if i == '?'
    e 'chop allows us to remove nucleotides from the main sequence.'
    return
  end
  i = 1 if i.nil? # Assign to the default then.
  i = i.to_i # Need a number past this point.
  if i == 0
    erev 'Please add a number, such as 1, or any other value.'
  else
    case chop_from_left_or_right_hand_side
    # ===================================================================== #
    # === :right
    # ===================================================================== #
    when :right,
         :default
      which_end = "3'"
    # ===================================================================== #
    # === :left
    # ===================================================================== #
    when :left
      which_end = "5'"
    end
    if dna_sequence_object?.size > 0
      erev "We will now remove some characters (#{simp(i.to_s)}#{rev}"\
           ") from the #{which_end} end of our main string."
    end
    if dna_sequence_object?.size == 0
      erev 'Can not remove anything as the sequence is empty.'
    elsif i > dna_sequence_object?.size
      erev 'We can not remove that many characters, thus we will'
      erev 'simply remove all characters now.'
      reset_string 
    else
      # =================================================================== #
      # Finally do the manipulation. We need to honour from which
      # side we will be operating on.
      # =================================================================== #
      case chop_from_left_or_right_hand_side
      # =================================================================== #
      # === :default
      # =================================================================== #
      when :default,
           :right
        # ================================================================= #
        # We also store the chopped-away sequence, but we have to be
        # mindful here since the sequence-object counts the nucleotides
        # differently than ruby counts Arrays.
        # ================================================================= #
        @internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[(-i)+1, i-1].dup
        seq_object?[-i, i] = ''
      # =================================================================== #
      # === :left
      # =================================================================== #
      when :left
        @internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[0, i].dup
        seq_object?[0, i+1] = ''
      end
    end
    unless dna_sequence_object?.size == 0
      erev "#{rev}The new length of the main string is now: "\
           "#{simp(dna_sequence_object?.size.to_s)}#{rev}."
    end
    show_dna_sequence
  end
end

#chop_to(i) ⇒ Object

#

chop_to

This method will chop up to the first occurence of the given input sequence.

If the given input sequence can not be found, no change is made.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4772

def chop_to(i)
  if i.is_a? Array
    i = i.first
  end
  i = i.to_s if i.is_a? Symbol # For instance: chop_to :ATG
  i.delete!(':') if i.include? ':'
  case i
  when 'start'
    i = 'ATG'
  end
  _ = nucleotide_sequence?
  if i.include? 'U'
    # ===================================================================== #
    # Convert Uracil to Thymine next.
    # ===================================================================== #
    erev "The given input sequence includes at the least one "\
         "#{sfancy('U')}#{rev}, which we will convert to #{sfancy('T')}#{rev}."
    i.tr!('U','T')
  end
  if _.include? i
    # ===================================================================== #
    # Ok, we found the search sequence, so now we can chop off the
    # unnecessary sequences.
    # ===================================================================== #
    position = _.index(i)
    erev "Chopping away #{sfancy(position.to_s)}#{rev} nucleotides from "\
         "the left-hand side (5' end) next."
    @internal_hash[:array_these_sequences_were_chopped_away] << seq_object?[0, position+1]
    seq_object?[0, position+1] = ''
    show_dna_sequence
  else
    erev 'No modification can be made as our target nucleotide sequence'
    erev "does not include the given search string #{sfancy(i)}."
  end
end

#chunked_display(i = dna_sequence? ) ⇒ Object

#

chunked_display

This method will show a “chunked” display of the nucleotides that is similar to the FASTA display at NCBI.

Invoke via:

cdisplay
#


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# File 'lib/bioroebe/shell/shell.rb', line 6805

def chunked_display(
    i = dna_sequence?
  )
  i = i.join if i.is_a? Array
  i = dna_sequence? if i.nil?
  i = dna_sequence? if i.empty?
  ::Bioroebe::GenbankFlatFileFormatGenerator.new(i) # bl $BIOROEBE/genbank/genbank_flat_file_format_generator.rb
end

#clear(i) ⇒ Object

#

clear

Functionality that is associated with clearing something, can be stored here.

Usage example:

clear highlighting
#


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# File 'lib/bioroebe/shell/shell.rb', line 8829

def clear(i)
  if i.is_a? Array
    i = i.join(' ').strip
  end
  case i
  when /^highlight/
    e 'Clearing all highlighting next.'
    set_highlight_colour nil
  end
end

#coding_area? ⇒ Boolean

#

coding_area?

Query method over the “coding area” that we will focus on. So for example, if we have 100 nucleotides, but the coding area says 3-34, then we will only care for the nucleotides starting at position 3 and ending at position 34.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8972

def coding_area?
  @internal_hash[:coding_area]
end

#codon(i = sequence? ) ⇒ Object Also known as: codons, codon?, codons?

#

codon

This method will identify codons.

Usage example from within the Shell:

codon AAAGUCCAU
#


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# File 'lib/bioroebe/shell/shell.rb', line 3253

def codon(
    i = sequence?
  )
  if i.is_a? Array # We don't want Arrays here.
    i = i.join.strip
  end
  if i.nil?
    i = sequence?
  else
    if i.is_a? String
      i = sequence? if i.empty?
    end
  end
  _ = nucleotides_to_aminoacid(i)
  erev _
end

#codon_to_aminoacid(i) ⇒ Object

#

codon_to_aminoacid

Translate a codon into an aminoacid through this method.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8418

def codon_to_aminoacid(i)
  Bioroebe.codon_to_aminoacid(i)
end

#colour_for_nucleotide(i = '') ⇒ Object Also known as: colour_for_nucleotides

#

colour_for_nucleotide

#


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# File 'lib/bioroebe/shell/shell.rb', line 2091

def colour_for_nucleotide(i = '')
  royalblue(i)
end

#colour_for_stop_codon(i) ⇒ Object

#

colour_for_stop_codon

#


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# File 'lib/bioroebe/shell/shell.rb', line 2084

def colour_for_stop_codon(i)
  orange(i)
end

#colour_scheme_demo(use_this_sequence = 'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC') ⇒ Object

#

colour_scheme_demo

#


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# File 'lib/bioroebe/shell/shell.rb', line 6567

def colour_scheme_demo(
    use_this_sequence = 'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC'
  )
  ColourSchemeDemo.new(use_this_sequence)
  file = ::Bioroebe::ColourSchemeDemo.create_demo_file.to_s
  erev file
  open_in_browser(file) if File.exist? file
end

#colour_scheme_for_aminoacids(i = aminoacid_sequence? ) ⇒ Object

#

colour_scheme_for_aminoacids

Invocation example:

caa TTTHGHGHGIHIHRGGGGAATTTTHGHGHGIHIHRGGGGAATTHGHGHGIHIHRGGGGAAATTT
#


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# File 'lib/bioroebe/shell/shell.rb', line 9541

def colour_scheme_for_aminoacids(
    i = aminoacid_sequence?
  )
  i = aminoacid_sequence? if i.nil?
  hash = ::Bioroebe::ColourScheme::Taylor.colours?
  tokens = i
  if tokens.is_a? String
    tokens = tokens.chars
    tokens = tokens.each_slice(80).to_a
  end
  # ======================================================================= #
  # Get it in chunks of 30.
  # ======================================================================= #
  n_chunks = 30
  chunks = tokens.each_slice(n_chunks).to_a
  e; chunks.each {|array|
    array.each {|entry|
      chars = entry.chars
      chars.each {|aminoacid|
        if hash.has_key? aminoacid
          value = hash[aminoacid]
          array = HexToRGB[value] # Obtain the R,G,B Array from here.
          ::Colours.rgb_print(array, aminoacid)
        else
          erev "The hash does not include the key #{simp(aminoacid)}#{rev}."
        end
      }
    }
    e
  }; e
end

#colour_scheme_for_nucleotides(i = dna_sequence? ) ⇒ Object

#

colour_scheme_for_nucleotides

This method can eventually be used to display the colour codes for the nucleotides.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6882

def colour_scheme_for_nucleotides(
    i = dna_sequence?
  )
  begin
    require 'roebe/classes/hex_to_rgb.rb'
  rescue LoadError; end
  if Object.const_defined?(:Roebe) and
     Roebe.const_defined?(:HexToRGB)
    i = dna_sequence? if i.nil?
    i = i.first if i.is_a? Array
    hash = ::Bioroebe::ColourScheme::Nucleotide.colours?
    tokens = i.chars
    # ===================================================================== #
    # Get it in chunks of 80.
    # ===================================================================== #
    chunks = tokens.each_slice(80).to_a
    e; chunks.each {|array|
      array.each {|char|
        if hash.has_key? char
          value = hash[char]
          array = Roebe::HexToRGB[value] # Obtain the R,G,B Array from here.
          ::Colours.rgb_print(array, char)
        end
      }
      e
    }; e
  else
    erev 'Please install the gem hex_to_rgb, in order '\
         'to use this method.'
  end
end

#colourize_fasta_file(i) ⇒ Object

#

colourize_fasta_file

Invocation example:

colourize_fasta_file /Depot/Temp/bioroebe/sequence.fasta
#


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# File 'lib/bioroebe/shell/shell.rb', line 3677

def colourize_fasta_file(i)
  if i.is_a? Array
    i.each {|entry| colourize_fasta_file(entry) }
  else
    # ===================================================================== #
    # First, get the raw content of the fasta sequence here.
    # ===================================================================== #
    if File.exist? i
      sequence = ::Bioroebe.parse_fasta_file(i).sequence?
      # =================================================================== #
      # Now that we have the sequence, colourize it.
      # =================================================================== #
      cliner {
        ColourSchemeDemo.new(sequence)
      }
    end
  end
end

#colourize_nucleotide(i, add_leading_five_and_trailing_three_primes = true) ⇒ Object Also known as: colourize_nucleotide_sequence

#

colourize_nucleotide

Assemble 5’-sequence-3’, with colours.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10998

def colourize_nucleotide(
    i,
    add_leading_five_and_trailing_three_primes = true
  )
  case add_leading_five_and_trailing_three_primes
  # ======================================================================= #
  # === :do_not_add_anything_else
  # ======================================================================= #
  when :do_not_add_anything_else,
       :make_no_modifications
    add_leading_five_and_trailing_three_primes = false
  end
  if add_leading_five_and_trailing_three_primes
    leading_5_prime+
    sfancy(i)+
    rev+
    trailing_3_prime
  else
    sfancy(i)+
    rev
  end
end

#colourize_this_aminoacid(i) ⇒ Object

#

colourize_this_aminoacid

Use this method to colourize any particular aminoacid.

This should make it easier to detect special aminoacids.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10935

def colourize_this_aminoacid(i)
  if i.nil?
    erev 'Please supply an argument, an aminoacid. Either one letter, '\
         'such as A for Alanine, or the full name.'
    return
  end
  unless ::Bioroebe.array_colourize_this_aminoacid.include? i
    erev 'We will now colourize the aminoacid `'+swarn(i)+'`.'
    ::Bioroebe.array_colourize_this_aminoacid << i
  end
end

#command_to_be_passed_to_the_menu? ⇒ Boolean

#

command_to_be_passed_to_the_menu?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7461

def command_to_be_passed_to_the_menu?
  @internal_hash[:command_to_be_passed_to_the_menu]
end

#compact_file(this_file = nil) ⇒ Object

#

compact_file

Delegate into class Bioroebe::Compacter.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7541

def compact_file(
    this_file = nil
  )
  ::Bioroebe::Compacter.new(this_file)
end

#compare_two_files(file_a, file_b) ⇒ Object

#

compare_two_files

We will here compare whether two files are identical.

First argument is the first file, second argument is the second file.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8518

def compare_two_files(file_a, file_b)
  if File.exist? file_a
    file_a = File.read(file_a)
  else
    erev file_a+' does not exist.'
  end
  if File.exist? file_b
    file_b = File.read(file_b)
  else
    erev file_b+' does not exist.'
  end
  erev (file_a == file_b)
end

#compare_two_strings_as_alignment(string1 = nil, string2 = nil) ⇒ Object

#

compare_two_strings_as_alignment

This allows us to interactively compare two strings.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8785

def compare_two_strings_as_alignment(
    string1 = nil,
    string2 = nil
  )
  if string1 and string2
    # Simply pass through in this case.
  else
    erev 'You desire to compare two strings.'
    e
    erev 'Please input the '+palegreen('first')+rev+' string/sequence now:'
    print '  '
    if has_readline?
      string1 = Readline.readline
    else
      string1 = $stdin.gets.chomp
    end
    erev 'Please input the '+palegreen('second')+rev+' string now:'
    print '  '
    if has_readline?
      string2 = Readline.readline
    else
      string2 = $stdin.gets.chomp
    end
  end
  # ======================================================================= #
  # Delegate into class SimpleStringComparer next.
  # ======================================================================= #
  _ = ::Bioroebe::SimpleStringComparer.new(:dont_run_yet) { :use_vertical_bar } # bl $BIOROEBE/string_matching/simple_string_comparer.rb
  _.string1 = string1
  _.string2 = string2
  _.compare
end

#compseq(i = dna_sequence? ) ⇒ Object

#

compseq

Analyze a given sequence via compseq.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5719

def compseq(
    i = dna_sequence?
  )
  i = dna_sequence? if i.nil?
  ::Bioroebe::Compseq.new(i) # bl $BIOROEBE/compseq.rb
end

#config? ⇒ Boolean Also known as: configuration?

#

config?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 9687

def config?
  @configuration
end

#consider_analysing_the_local_dataset_on_startup ⇒ Object

#

consider_analysing_the_local_dataset_on_startup

This method will analyse the local dataset (should it exist), and then display some information to the user about it.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5217

def consider_analysing_the_local_dataset_on_startup
  if @internal_hash and
     @internal_hash.has_key?(:analyse_the_local_dataset_on_startup) and
     @internal_hash[:analyse_the_local_dataset_on_startup]
    Bioroebe::AnalyseLocalDataset.new
  end
end

#consider_assigning_the_default_dna_sequence_from_a_yaml_file ⇒ Object

#

consider_assigning_the_default_dna_sequence_from_a_yaml_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 1239

def consider_assigning_the_default_dna_sequence_from_a_yaml_file
  if defined? DEFAULT_DNA_INPUT_YAML_FILE # Main DNA string.
    set_string(DEFAULT_DNA_INPUT_YAML_FILE)
  end
end

#considering_changing_the_title_of_the_kde_konsole_tab(to_this_title = 'BioRoebe') ⇒ Object

#

considering_changing_the_title_of_the_kde_konsole_tab

#


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# File 'lib/bioroebe/shell/shell.rb', line 8101

def considering_changing_the_title_of_the_kde_konsole_tab(
    to_this_title = 'BioRoebe'
  )
  if ::Bioroebe.try_to_rename_kde_konsole? and
     Object.const_defined? :Roebe # For project roebe.
    require 'roebe/classes/kde/kde_konsole/kde_konsole.rb'
    Roebe.change_konsole_tab_title(to_this_title, :be_silent)
  end
end

#convert_five_prime_dna_into_five_prime_mrna(this_string = sequence? ) ⇒ Object

#

convert_five_prime_dna_into_five_prime_mrna (DNA to mRNA)

This method will translate the 5’-DNA into 5’-mRNA.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6142

def convert_five_prime_dna_into_five_prime_mrna(
    this_string = sequence?
  )
  erev padding?+leading_5_prime+
       sfancy(this_string.upcase.tr('T','U'))+
       rev+trailing_3_prime
end

#copy_bioroebe_shell_before_quitting ⇒ Object

#

copy_bioroebe_shell_before_quitting

Use this method to copy the Bioroebe shell before quitting.

We will make use of class InstallRubyProject for this.

This was disabled as of Jan 2016. The reason is that it confuses me too much, seriously. Perhaps I will re-enable it again at a later time.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8209

def copy_bioroebe_shell_before_quitting
  _ = RUBY_SRC+'bioroebe/'
  begin
    require 'roebe/classes/install_ruby_project.rb'
  rescue LoadError; end
  if Object.const_defined? :Roebe
    irp = Roebe::InstallRubyProject.new(_, false)
    irp.run
  elsif on_roebe?
    erev 'The project custom_methods/install_ruby_project is not available.'
    erev 'We will install it now.'
    cd '$RSRC/roebe/'
    Easycompile.rinstall2 if Object.const_defined? :Easycompile
  end if false # Disabled it here. Not sure if I will re-enable it.
end

#could_this_be_an_amino_acid?(i) ⇒ Boolean

#

could_this_be_an_amino_acid?

If the input is an amino acid, we return true for this method here.

Characters such as ‘?’ will be removed.

Invocation examples:

phenylalanine
glycin
glycine
#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6770

def could_this_be_an_amino_acid?(i)
  i = i.to_s.downcase
  i.delete!('?') if i.include? '?' # Get rid of '?' tokens.
  return_value = false
  unless i.empty?
    # ===================================================================== #
    # First, we check here for german names. These names are kept in
    # the file called
    # 'amino_acids_long_name_to_one_letter.yml'
    # ===================================================================== #
    unless AMINO_ACIDS_RESTE.has_key?(i)
      if AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.has_key?(i)
        i = AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER[i]
        i = AMINO_ACIDS_ENGLISH[i].downcase
      end
    end
    if AMINO_ACIDS_RESTE.has_key?(i)
      return_value = true
    end
  end
  return return_value
end

#count_amount_of_aminoacids(i) ⇒ Object

#

count_amount_of_aminoacids

#


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# File 'lib/bioroebe/shell/shell.rb', line 2979

def count_amount_of_aminoacids(i)
  ::Bioroebe::CountAmountOfAminoacids.new(i)
end

#create_balanced_composition(i = nil) ⇒ Object

#

create_balanced_composition

This method will create a balanced nucleotide-composition.

In other words, we can do a DNA string with 25% A, G, C, T each.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4221

def create_balanced_composition(i = nil)
  string = ''.dup # The return string.
  if i.nil?
    n_nucleotides_to_be_generated = 1000 # Default.
    # In this case, go interactive.
    erev 'Please enter the percentage of each nucleotide next.'
    ee 'A: '
    a = $stdin.gets.chomp.to_i
    ee 'T: '
    t = $stdin.gets.chomp.to_i
    ee 'C: '
    c = $stdin.gets.chomp.to_i
    erev 'G is automatically calculated.'
    g = 100 - (a + t + c)
    ee 'G: '
    # The following is not yet finished.
    string << ('A' * a)+('T' * t)+('C' * c)+('G' * g)
  else
    i = 1000 if i.nil? or (i.is_a?(Array) and i.empty?) # The default.
    n_nucleotides_to_be_generated = i
    # ===================================================================== #
    # Otherwise, we assume it to be 25% for each nucleotide. The following
    # code will ensure that.
    # ===================================================================== #
    n_times = n_nucleotides_to_be_generated.to_i / 4
    n_times.times {
      _ = return_dna_nucleotides # Get all four entries first.
      _.shuffle.each {|nucleotide|
        string << nucleotide
      }
    }
  end
  erev "Note: we will assume the target size will "\
       "be #{n_nucleotides_to_be_generated.to_s} nucleotides."
  return string # The nucleotide-string to be returned.
end

#create_fasta_file ⇒ Object

#

create_fasta_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 6065

def create_fasta_file
  set_save_file :default_fasta
  e 'Now creating a new fasta file. Will store into `'+sfile(@save_file)+'`.'
  _ = '>gi|12345|pir|TVHGG| some unknown protein'+N
  _ << string?
  save_file(_, @internal_hash[:save_file])
end

#create_file(i = a?) ) ⇒ Object

#

create_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 3373

def create_file(i = a?)
  [i].flatten.each {|this_file|
    unless File.exist?(this_file)
      erev 'Creating the file '+sfile(this_file)+rev+' next.'
      FileUtils.touch(this_file)
    end
  }
end

#create_n_random_amino_acids(n = 1000) ⇒ Object

#

create_n_random_amino_acids

#


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# File 'lib/bioroebe/shell/shell.rb', line 7581

def create_n_random_amino_acids(n = 1000)
  set_aminoacids :random, n, :be_verbose
end

#cut(i) ⇒ Object

#

cut (cut tag)

This method will cut away some part from the DNA string.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3455

def cut(i)
  i = i.to_i
  sequence?[-i,i] = ''
  show_dna_sequence
end

#cut_at(this_sequence = 'GAATTC', be_verbose = true) ⇒ Object

#

cut_at

Use this method to chop off or rather cut at a DNA sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10487

def cut_at(
    this_sequence = 'GAATTC',
    be_verbose    = true
  )
  main_sequence = dna_sequence_object?
  this_sequence = this_sequence.join.strip if this_sequence.is_a? Array
  if be_verbose
    erev "We will chop away (at) the sequence #{simp(this_sequence)}#{rev}."
    erev 'Note that the sequences all originated from the larger '\
         'parent sequence.'
  end
  results = main_sequence.split(/#{this_sequence}/)
  results.each {|sequence|
    _ = properly_spaced_dna(sequence)
    _ << (' ('+sequence.size.to_s+' nucleotides)').rjust(110 - sequence.size)
    erev _
  }
end

#cut_sequence_in_slices_of(threshold = '9') ⇒ Object

#

cut_sequence_in_slices_of

This method cuts the sequence into slices of n, where n is the argument to this method.

So if you input 10 as argument, then we will put the nucleotides into chunks of 10 nucleotides per row.

Usage examples:

cut_sequence_in_slices_of 5
cut_sequence_in_slices_of 6
cut_sequence_in_slices_of 7
#


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# File 'lib/bioroebe/shell/shell.rb', line 7489

def cut_sequence_in_slices_of(
    threshold = '9'
  )
  _ = dna_sequence_object?
  matches = _.scan(/.{#{threshold}}/)
  matches.each {|entry|
    erev "  #{entry}"
  }
end

#cut_with_enzyme(i) ⇒ Object

#

cut_with_enzyme

#


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# File 'lib/bioroebe/shell/shell.rb', line 3506

def cut_with_enzyme(i)
  i = i.join(' ').strip if i.is_a? Array
  pp sequence_object?.cut_with_enzyme(i)
end

#cutseq(i = [1,3]) ⇒ Object

#

cutseq

This can be used to modify the sequence object. It will cut some segment out from the nucleotide.

Usage examples:

random 30; cutseq 5 8
random 30; cutseq 5-8
#


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# File 'lib/bioroebe/shell/shell.rb', line 3473

def cutseq(i = [1,3])
  if i.is_a? Array
    if i.size == 1 and i.first.is_a? String and i.first.include?('-')
      i = [i.first.split('-')].flatten
    end
    if i.empty? # In this case we will ask the user for input.
      erev 'No argument was provided. Please input the start nucleotide position next:'
      start_position = $stdin.gets.chomp.to_i
      erev 'Next, input the end nucleotide position:'
      end_position   = $stdin.gets.chomp
    elsif i.size > 1
      start_position = i.first
      end_position   = i.last
    end
  end
  # ======================================================================= #
  # === Handle +3 relational position given
  # ======================================================================= #
  if end_position.is_a? String and end_position.include?('+')
    end_position = start_position + end_position.delete('+').to_i
  end
  n_nucleotides_will_be_deleted = (end_position.to_i - start_position.to_i)+1
  # ======================================================================= #
  # Notify the user what we will do next.
  # ======================================================================= #
  erev 'Next cutting away '+simp(n_nucleotides_will_be_deleted.to_s)+
        rev+' nucleotides.'
  sequence_object?[start_position, end_position] = ''
end

#cytosin? ⇒ Boolean

#

cytosin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8339

def cytosin?
  YAML.load_file(FILE_NUCLEOTIDES)['Cytosin']
end

#dalton(i) ⇒ Object

#

dalton

This method will calculate the weight of several aminoacids, in Dalton. We assume that each aminoacid will have a weight of 110 Dalton.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9944

def dalton(i)
  n_dalton = i.to_f * 110
  e sfancy(i.to_s)+rev+' aminoacids have a molecular weight of '+
    simp(n_dalton.to_s)+rev+' Dalton ('+(n_dalton/1000.0).to_s+' kDa).'
end

#deduce_this_aminoacid_sequence(i = 'Lys-Ser-Pro-Ser-Leu-Asn-Ala-Ala-Lys', show_the_rna_sequence = true) ⇒ Object

#

deduce_this_aminoacid_sequence

Thi method will show the possible codons for an aminoacid sequence.

It will display the result in an ASCII table, on the commandline.

Trigger this like so:

sof
sof Lys-Ser-Pro-Ser-Leu-Asn-Ala-Ala-Lys
sof Thr Thr Glu Ala Val Glu Ser Thr Val Ala Thr Leu Glu Asp Ser
sof T-T-G-A-V-G-S-T-V
#


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# File 'lib/bioroebe/shell/shell.rb', line 4653

def deduce_this_aminoacid_sequence(
    i                     = 'Lys-Ser-Pro-Ser-Leu-Asn-Ala-Ala-Lys',
    show_the_rna_sequence = true
  )
  if i.nil? # This is the default.
    if aminoacid_sequence?
      i = aminoacid_sequence?
    else
      i = 'Lys-Ser-Pro-Ser-Leu-Asn-Ala-Ala-Lys'
    end
  end
  DeduceAminoacidSequence.new(i, show_rna: show_the_rna_sequence) # bl DeduceAminoacidSequence
end

#default_length? ⇒ Boolean

#

default_length?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7311

def default_length?
  @internal_hash[:default_length]
end

#design_polylinker(optional_length_of_polylinker = nil, be_verbose = true) ⇒ Object

#

design_polylinker

This method will design a polylinker from 3-8 random restriction enzymes sites.

You can pass a first argument to this method.

Example:

design_polylinker 100
#


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# File 'lib/bioroebe/shell/shell.rb', line 8637

def design_polylinker(
    optional_length_of_polylinker = nil,
    be_verbose                    = true
  )
  if optional_length_of_polylinker.is_a? Array
    optional_length_of_polylinker = optional_length_of_polylinker[0]
  end
  if optional_length_of_polylinker.nil?
    optional_length_of_polylinker = 20
  end
  optional_length_of_polylinker = optional_length_of_polylinker.to_i
  full_sequence = ''
  n_restriction_sites = rand(6)+3
  n_restriction_sites.times {
    full_sequence << return_random_restriction_enzyme(be_verbose)
  }
  if full_sequence.size < optional_length_of_polylinker
    loop {
      full_sequence << return_random_restriction_enzyme(be_verbose)
      break if full_sequence.size > optional_length_of_polylinker
    }
  end
  erev 'Our generated polylinker has '+sfancy(n_restriction_sites.to_s)+
       ' sites for restriction enzymes available (DNA Sequence '+
       'length is: '+full_sequence.size.to_s+').'
  erev 'We will also assign this sequence as the new DNA sequence.'
  assign_dna_sequence(full_sequence, :be_quiet)
  return full_sequence
end

#designate_this_input_as_coding_entry(i) ⇒ Object

#

designate_this_input_as_coding_entry

Invocation example:

coding_entry 51..3251
#


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# File 'lib/bioroebe/shell/shell.rb', line 5964

def designate_this_input_as_coding_entry(i)
  if i.is_a? Array
    i = i.first
  end
  if i.include? '..'
    # ===================================================================== #
    # Assume Range-behaviour here.
    # ===================================================================== #
    @internal_hash[:coding_area] = i
  end
  erev "Using the coding-area #{sfancy(i)}#{rev}."
  erev 'You can test this by e. g. invoking '+sfancy('ORF?')+rev+'.'
end

#determine_and_report_all_stop_codons ⇒ Object

#

determine_and_report_all_stop_codons

#


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# File 'lib/bioroebe/shell/shell.rb', line 1541

def determine_and_report_all_stop_codons
  dna_sequence = dna_sequence_object?
  erev 'Because 3 different stop codons exist, we have '\
       'to do '+slateblue('3 runs')+rev+'.'
  stop_codons?.each {|this_stop_codon|
    array_matches = ::Bioroebe.return_all_substring_matches(
      dna_sequence, this_stop_codon
    )
    if array_matches.empty?
      erev 'No match has been found.'
    else
      start_position = array_matches.last.first
      erev 'For the stop codon '+sfancy(this_stop_codon)+rev+' the last codon'
      erev 'occurrs at position '+simp(start_position.to_s)+rev+'.'
    end
  }
end

#disable(i) ⇒ Object

#

disable (disable tag)

#


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# File 'lib/bioroebe/shell/shell.rb', line 9727

def disable(
    i
  )
  if i.is_a? Array
    i = i.join(' ').strip
  end
  case i.to_s # case tag
  # ======================================================================= #
  # === disable colours
  # ======================================================================= #
  when 'colours',
       'colors',
       /^col/
    disable_colours
  # ======================================================================= #
  # === disable :cd_aliases
  # ======================================================================= #
  when /^-?-?cd(-|_)?aliases$/i
    erev 'We will no longer use class Rcfiles::DirectoryAliases'
    ::Bioroebe::Configuration.do_not_use_expand_cd_aliases
  # ======================================================================= #
  # === truncate
  # ======================================================================= #
  when /^truncate$/i
    disable_truncate
  # ======================================================================= #
  # === prompt
  # ======================================================================= #
  when 'prompt'
    set_prompt :empty # This means to use an empty prompt.
  # ======================================================================= #
  # === padding
  # ======================================================================= #
  when 'padding'
    set_padding 0, :be_verbose
  # ======================================================================= #
  # === disable xsel
  # ======================================================================= #
  when 'xsel'
    disable_xsel
  else
    erev "No such disable-action could be found (#{sfancy(i)}#{rev})"
  end
end

#disable_colours_in_an_extended_manner(be_verbose = :be_quiet) ⇒ Object Also known as: disable_enable_colours, extended_disable_colours

#

disable_colours_in_an_extended_manner (disable tag)

#


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# File 'lib/bioroebe/shell/shell.rb', line 703

def disable_colours_in_an_extended_manner(
    be_verbose = :be_quiet
  )
  disable_colours(be_verbose)
  ::Bioroebe.disable_colours
  @highlight_colour = '' # Use this colour to highlight important sequences.
  set_prompt
end

#disable_truncate ⇒ Object

#

disable_truncate

#


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# File 'lib/bioroebe/shell/shell.rb', line 8709

def disable_truncate
  do_not_truncate
end

#disable_xsel ⇒ Object

#

disable_xsel

#


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# File 'lib/bioroebe/shell/shell.rb', line 9233

def disable_xsel
  if use_xsel?
    e 'Now disabling xsel.'
    @internal_hash[:use_xsel] = false
  else
    e 'xsel is already disabled.'
  end
end

#discover_all_palindromes(i = dna_sequence?, , min = 4, max = 10) ⇒ Object

#

discover_all_palindromes

We need to discover all palindromes. For this, we need a min and a max value.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7635

def discover_all_palindromes(
    i   = dna_sequence?,
    min =  4,
    max = 10
  )
  i = dna_sequence? unless i
  case i # case tag
  when 'default',
       ':default'
    i = dna_sequence?
  end
  @internal_hash[:array_palindromes] = [] # We store the Palindromes in this Array.
  n_times = i.size

  min.upto(max) {|length|
    # ===================================================================== #
    # First, iterate by starting over the min value.
    # ===================================================================== #
    n_times.times {|counter|
      possible_palindrome_sequence = i[counter, length]
      counter += 1 # Adding +1 because nucleotides start at 1, not 0.
      if ::Bioroebe.is_palindrome?(possible_palindrome_sequence) and
         (possible_palindrome_sequence.size >= length)
        @internal_hash[:array_palindromes] << [possible_palindrome_sequence, counter]
      end
    }
  }
  e; erev 'Starting nucleotide | Palindrome sequence'; e
  @internal_hash[:array_palindromes].each {|array|
    index_position = array.last
    nucleotides    = array.first
    erev '                 '+index_position.to_s.rjust(3)+' '+
         nucleotides+' ('+swarn(nucleotides.size.to_s)+rev+')'
  }; e
end

#display_all_aminoacids ⇒ Object

#

display_all_aminoacids

This method will display all Aminoacids.

Invocation example:

daminoacids
#


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# File 'lib/bioroebe/shell/shell.rb', line 9307

def display_all_aminoacids
  e
  erev 'Aminoacids Shortnames:'
  erev # Newline here is ok.
  aa = ::Bioroebe::AMINO_ACIDS # Is a hash.
  aa.keys.sort.each {|key|
    result = aa[key].select {|inner_key, value| inner_key.size == 3 }.values.first
    erev '  '+key+': '+sfancy(result)
  }; e # Trailing newline.
end

#display_glycolysis_pathway ⇒ Object

#

display_glycolysis_pathway

This method will show the glycolysis Pathway.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10109

def display_glycolysis_pathway
  array = Pathways.glycolysis_pathway # Obtain the glyclosis pathway, as Array.
  if Object.const_defined? :Display
    Display.display(array, ')')
  else
    array.each {|entry| e ' - '+entry }
  end
end

#display_nucleotide_sequence(this_sequence = dna_sequence_object?, , &block) ⇒ Object Also known as: display_this_nucleotide_sequence, display_this_sequence, show_this_sequence

#

display_nucleotide_sequence

Consistently use this method whenever you wish to display a nucleotide sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1836

def display_nucleotide_sequence(
    this_sequence = dna_sequence_object?,
    &block
  )
  case this_sequence
  when :default
    this_sequence = dna_sequence_object?
  end
  do_show_piped_output = false
  if block_given?
    yielded = yield
    case yielded
    when :piped,
         :show_piped
      do_show_piped_output = true
    end
  end
  hash = {
    padding_to_use:    padding?,
    show_piped_output: do_show_piped_output
  }
  show_nucleotide_sequence?.report_this_sequence(this_sequence) { hash }
end

#display_open_reading_frames(i = dna_sequence_object?, , &block) ⇒ Object

#

display_open_reading_frames

Invocation example:

display_open_reading_frames ATGAGCAAGGCCGACTACGAGAAG
#


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# File 'lib/bioroebe/shell/shell.rb', line 5946

def display_open_reading_frames(
    i = dna_sequence_object?, &block
  )
  i = i.first if i.is_a? Array
  i = dna_sequence_object? if i.nil?
  i = dna_sequence_object? if i.empty?
  require 'bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb'
  ::Bioroebe::DisplayOpenReadingFrames.new(i, &block)
end

#dna_padding(this_sequence, get_rid_of_spaces = false) ⇒ Object Also known as: properly_spaced_dna, properly_padded_dna_string

#

dna_padding (dna_padding tag)

This method will properly pad a DNA string (with leading 5’ and trailing 3’). That string will be returned.

First argument should be the string (sequence) that you wish to modify.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9260

def dna_padding(
    this_sequence,
    get_rid_of_spaces = false
  )
  return left_pad?+
         five_prime(get_rid_of_spaces)+rev+
         sfancy(this_sequence)+rev+
         trailer(get_rid_of_spaces)
end

#dna_sequences? ⇒ Boolean Also known as: array_sequences?

#

dna_sequences?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8362

def dna_sequences?
  @internal_hash[:array_dna_sequences]
end

#dna_to_aminoacid_sequence(i = dna_sequence? ) ⇒ Object

#

dna_to_aminoacid_sequence

Convert a DNA sequence into the corresponding aminoacid sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6014

def dna_to_aminoacid_sequence(
    i = dna_sequence?
  )
  i = dna_sequence? if i.nil?
  i = dna_sequence? if i.empty?
  ::Bioroebe::DnaToAminoacidSequence.new(i)
end

#dna_translate(i) ⇒ Object

#

dna_translate

#


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# File 'lib/bioroebe/shell/shell.rb', line 10823

def dna_translate(i)
  i = i.join(' ').strip if i.is_a? Array
  if i.nil? or i.empty?
    if dna_sequence_as_string?
      i = dna_sequence_as_string?
      erev 'Using the current DNA sequence (size: '+
           i.size.to_s+' nucleotides)'
      # =================================================================== #
      # assign_dna_sequence(i, :be_verbose) # First assign
      # ^^^ Why would we want to re-assign here? Makes no sense, thus it
      #     was disabled as of December 2021. 
      # =================================================================== #
    end
  end
  # ======================================================================= #
  # Find and display the complement to this DNA sequence:
  # ======================================================================= #
  erev "The #{orange('complementary DNA Strand')}#{rev} is:"
  e
  show_nucleotide_sequence?.display(i) { :complementary_strand }
  e
end

#dna_with_ends(i = dna_sequence_as_string?, , optional_colourize = nil, colourize_everything = true) ⇒ Object

#

dna_with_ends

Display DNA with proper ends.

The first argument should be the string that we will colourize.

If the second argument is given (‘optional_colourize`), then this method will colourize the sequence at certain positions. This can be useful to display, for instance, restriction-sites.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9855

def dna_with_ends(
    i                    = dna_sequence_as_string?,
    optional_colourize   = nil,
    colourize_everything = true
  )
  i.upcase! if config?.respond_to?(:upcase_nucleotides) and config?.upcase_nucleotides
  if optional_colourize.is_a? String
    optional_colourize = [optional_colourize]
  end
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :honour_coding_area_if_it_exists
    # ===================================================================== #
    when :honour_coding_area_if_it_exists
      if optional_colourize and @internal_hash[:coding_area]
        # ================================================================= #
        # We will colourize based on the coding area that was designated.
        # ================================================================= #
        _ = @internal_hash[:coding_area]
        # ================================================================= #
        # We deduct 1 because ruby Arrays start at 0.
        # ================================================================= #
        start_position = _.split('..').first.to_i - 1
        end_position   = _.split('..').last.to_i  - 1
        internal_segment = i[start_position .. end_position]
        use_this_as_return_string = ''
        use_this_as_return_string << i[0..(start_position-1)]
        optional_colourize.each {|inner_entry|
          internal_segment.gsub!(inner_entry, yellow+inner_entry+rev)
        }
        use_this_as_return_string << internal_segment
        use_this_as_return_string << i[(end_position+1) .. -1]
        i = use_this_as_return_string
      elsif optional_colourize
        # ================================================================= #
        # Apply all entries given in the Array.
        # ================================================================= #
        if optional_colourize.is_a? Array
          optional_colourize.flatten.each {|inner_entry|
            i.gsub!(
              inner_entry, colour_for_stop_codon(inner_entry)+rev
            ) # Colourize in yellow.
          }
        else
          # =================================================================== #
          # Make sure that we have a String past this point.
          # =================================================================== #
          optional_colourize = optional_colourize.to_s
          if colourize_everything == true
            i.gsub!(optional_colourize, colour_for_stop_codon(optional_colourize)+rev)
          else
            if colourize_everything == 1
              i.sub!(optional_colourize, colour_for_stop_codon(optional_colourize)+rev)
            end
          end
        end
      end
    end
  else
    i = "#{sfancy(i)}#{rev}"
  end
  # ======================================================================= #
  # We will report the DNA sequence with leading 5' prime and
  # trailing 3' prime.
  # ======================================================================= #
  return "#{leading_five_prime}#{i}#{trailing_three_prime}"
end

#do_a_silent_startup ⇒ Object Also known as: do_silent_startup

#

do_a_silent_startup

Use this method when you want to perform a silent startup.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8077

def do_a_silent_startup
  @internal_hash[:silent_startup] = true
end

#do_action(*i) ⇒ Object

#

do_action

Usage example:

do not truncate
#


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# File 'lib/bioroebe/shell/shell.rb', line 7169

def do_action(*i)
  if i.is_a? Array
    i.flatten!
  end
  first_argument  = i[0]
  second_argument = i[1]
  case second_argument
  when 'truncate'
    do_not_truncate if first_argument == 'not'
  end
end

#do_analyze_sequence(i = sequence? ) ⇒ Object

#

do_analyze_sequence

Use this method to find unique sequences.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4984

def do_analyze_sequence(
    i = sequence?
  )
  if i.is_a?(Array) and i.empty?
    i = sequence?
  end
  if i.empty? and (!aminoacid_sequence?)
    erev 'Please first assign a sequence.'
  elsif aminoacid_sequence?
    aminoacid_sequence = aminoacid_sequence?
    show_protein_composition(aminoacid_sequence)
    # ===================================================================== #
    # Also show the molecular mass.
    # ===================================================================== #
    molecular_mass_of_amino_acids_in_this_sequence(aminoacid_sequence)
  else
    erev 'Searching for '+steelblue('NLS sequences')+rev+' first:'
    run_nls_search
  end
end

#do_mutate_dna_sequence_at_this_nucleotide_position(this_nucleotide_position = 1, new_nucleotide = nil, old_sequence = dna_sequence? ) ⇒ Object

#

do_mutate_dna_sequence_at_this_nucleotide_position

You can use this method to mutate a DNA sequence at a given position.

The first argument should be the specific nucleotide position that you wish to modify. Keep in mind that in BioRoebe we will start to count at nucleotide position 1; in ruby Arrays, we would start to count at position 0 but DNA sequences don’t have a nucleotide called 0 by definition, hence why we use a more (bio)logical way that makes more sense.

Usage example:

random 15; mutate 1
#


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# File 'lib/bioroebe/shell/shell.rb', line 5022

def do_mutate_dna_sequence_at_this_nucleotide_position(
    this_nucleotide_position = 1,
    new_nucleotide           = nil,
    old_sequence             = dna_sequence?
  )
  if this_nucleotide_position.is_a? Array
    new_nucleotide = this_nucleotide_position[1] if this_nucleotide_position.size > 1
    this_nucleotide_position = this_nucleotide_position.first
  end
  # ======================================================================= #
  # === this_nucleotide_position must be a Fixnum past that point
  # ======================================================================= #
  this_nucleotide_position = this_nucleotide_position.to_i
  if this_nucleotide_position < 1
    this_nucleotide_position = 1 # 1 is minimum.
  end
  old_nucleotide = old_sequence[this_nucleotide_position-1, 1]
  unless new_nucleotide # Enter this clause if new_nucleotide is nil.
    new_nucleotide = (DNA_NUCLEOTIDES - [old_nucleotide]).sample # Obtain a random but different nucleotide.
  end
  erev 'At nucleotide position '+sfancy(this_nucleotide_position.to_s)+
       rev+' we will replace '+simp(old_nucleotide)+rev+' with '+
       simp(new_nucleotide)+rev+'.'
  old_sequence[this_nucleotide_position-1, 1] = new_nucleotide
  set_dna_sequence(old_sequence) # We'll also assign this.
end

#do_not_show_the_leader(be_verbose = true) ⇒ Object

#

do_not_show_the_leader

#


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# File 'lib/bioroebe/shell/shell.rb', line 5824

def do_not_show_the_leader(
    be_verbose = true
  )
  if be_verbose
    e "The 3'-trailer of nucleotide sequences will not be shown."
  end
  @internal_hash[:show_the_leader] = false
end

#do_not_show_the_trailer(be_verbose = true) ⇒ Object

#

do_not_show_the_trailer

#


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# File 'lib/bioroebe/shell/shell.rb', line 5812

def do_not_show_the_trailer(
    be_verbose = true
  )
  if be_verbose
    e "The 3'-trailer of nucleotide sequences will not be shown."
  end
  @internal_hash[:show_the_trailer] = false
end

#do_not_truncate ⇒ Object

#

do_not_truncate

#


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# File 'lib/bioroebe/shell/shell.rb', line 9351

def do_not_truncate
  ::Bioroebe.do_not_truncate
  erev 'We will no longer truncate too-long output.'
end

#do_not_use_working_directory_as_prompt ⇒ Object

#

do_not_use_working_directory_as_prompt

#


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# File 'lib/bioroebe/shell/shell.rb', line 5101

def do_not_use_working_directory_as_prompt
  @internal_hash[:use_working_directory_as_prompt] = false
end

#do_open(i) ⇒ Object

#

do_open

Open an URL - via browser.

#


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# File 'lib/bioroebe/shell/shell.rb', line 11026

def do_open(i)
  case i
  when 'all','ALL'
    open_my_files
  else # Default.
    open_in_browser(i)
  end
end

#do_quit(determine_what_to_do = exit_the_shell_how? ) ⇒ Object

#

do_quit (exit tag, quit tag)

Consistently use this method when quitting from the shell. No exception!

On quitting, we may copy the bioroebe-files.

We may either return a symbol, or we may simply call exit.

#


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# File 'lib/bioroebe/shell/shell.rb', line 11725

def do_quit(
    # ===================================================================== #
    # The variable that comes next is usually a Symbol.
    # ===================================================================== #
    determine_what_to_do = exit_the_shell_how?
  )
  # ======================================================================= #
  # We can also copy the content of the Bioroebe-Project - but I am
  # not sure if this is worth the trade-off, so it was disabled again.
  # ======================================================================= #
  # copy_bioroebe_shell_before_quitting
  # ======================================================================= #
  considering_changing_the_title_of_the_kde_konsole_tab('')
  case determine_what_to_do
  when :instantly,
       nil
    :break
  else # This is valid for :exit_gracefully.
    return determine_what_to_do # Allo a graceful exit.
  end
end

#do_start_the_sinatra_interface ⇒ Object

#

do_start_the_sinatra_interface

Invocation example:

biosh --sinatra
#


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# File 'lib/bioroebe/shell/shell.rb', line 3184

def do_start_the_sinatra_interface
  require 'bioroebe/sinatra/sinatra_wrapper.rb'
  ::Bioroebe.start_sinatra_interface
end

#do_toggle_debug_value ⇒ Object

#

do_toggle_debug_value

#


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# File 'lib/bioroebe/shell/shell.rb', line 6034

def do_toggle_debug_value
  if @internal_hash[:debug]
    @internal_hash[:debug] = false
  else
    @internal_hash[:debug] = true
  end
end

#do_truncate? ⇒ Boolean

#

do_truncate?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 9333

def do_truncate?
  ::Bioroebe.do_truncate?
end

#do_use_working_directory_as_prompt ⇒ Object Also known as: use_working_directory_as_prompt

#

use_working_directory_as_prompt

Use this method if you wish to use the working-directory as your prompt.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8686

def do_use_working_directory_as_prompt
  @internal_hash[:use_working_directory_as_prompt] = true
end

#does_this_remote_file_exist?(i) ⇒ Boolean

#

does_this_remote_file_exist?

This method determines, based on wget, whether a remote file exists or whether it does not.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 10284

def does_this_remote_file_exist?(i)
  remote_file_exists = false
  # ======================================================================= #
  # Use wget --spider to check if the remote file exists.
  # ======================================================================= #
  _ = "wget --spider -v #{i} 2>&1"
  result = `#{_}`
  if result.include?('Remote file exists') or # Yes, the remote file exists.
     result =~ /File '.+' exists./
    remote_file_exists = true
  end
  if result.include? '/404'
    remote_file_exists = false
  end
  return remote_file_exists
end

#downcase_main_string ⇒ Object

#

downcase_main_string (downcase tag, dcase tag)

Use this method to downcase the main sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6929

def downcase_main_string
  downcased_sequence = seq?.downcase
  set_sequence(
    downcased_sequence
  )
end

#download(i) ⇒ Object

#

download (download tag)

General download handler. Some sequences will be changed, such as lambda (for the phage called lambda), to the corresponding entry at NCBI.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3518

def download(i)
  if i.is_a? Array
    i.each {|entry| download(entry) }
  else
    case i.to_s
    # ===================================================================== #
    # === The lambda phage sequence
    #
    # Download the lambda-sequence, via:
    #
    #   download lambda
    #
    # ===================================================================== #
    when 'lambda',
         /^-?-?lambda(_|-)?genome$/i
      i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_001416.1.fasta')+
          '.fasta'
    # ===================================================================== #
    # === Download the cytochrome c sequence (of humans)
    #
    # This should be equivalent to:
    #
    #   https://www.ncbi.nlm.nih.gov/protein/XP_011521207.1?report=fasta
    #
    # ===================================================================== #
    when /cytochrome_c_protein_sequence/
      return Bioroebe::Ncbi.efetch_by_url('NP_061820.1')
    # ===================================================================== #
    # === P1
    # ===================================================================== #
    when 'P1'
      i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_005856.1.fasta')+
          '.fasta'
    # ===================================================================== #
    # === P2
    #
    # The P2 phage, from E. coli, a temperate phage.
    # ===================================================================== #
    when 'P2'
      i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_041848.1.fasta')+
          '.fasta'
    # ===================================================================== #
    # === T12
    #
    # This is the Streptococcus phage T12.
    # ===================================================================== #
    when 'T12'
      i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_028700.1.fasta')+
          '.fasta'
    # ===================================================================== #
    # === T2
    #
    # This is the phage T2.
    # ===================================================================== #
    when 'T2'
      i = ::Bioroebe.map_ncbi_entry_to_eutils_id('AP018813.1.fasta')+
          '.fasta'
    # ===================================================================== #
    # === T4
    #
    # This is the phage T4.
    # ===================================================================== #
    when 'T4'
      i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_000866.4.fasta')+
          '.fasta'
    # ===================================================================== #
    # === T6
    #
    # This is the phage T6.
    # ===================================================================== #
    when 'T6'
      i = ::Bioroebe.map_ncbi_entry_to_eutils_id('MH550421.1.fasta')+
          '.fasta'
    # ===================================================================== #
    # === rhinovirus
    # ===================================================================== #
    when /^-?-?rhinovirus/i
      i = ::Bioroebe.map_ncbi_entry_to_eutils_id('NC_038311')+
          '.fasta'
    # ===================================================================== #
    # === Handle .pdb files here
    # ===================================================================== #
    when /\.pdb$/
      cd :download_directory
      wget i
      register_this_download(i)
      parse_this_pdb_file(File.basename(i))
    end
    # ===================================================================== #
    # === Handle Fasta files next
    # ===================================================================== #
    if i.end_with? '.fa' or i.end_with? '.fasta'
      i = i.dup if i.frozen?
      unless File.exist? i
        _ = Bioroebe::Ncbi.efetch_by_url(
             i.delete_suffix('.fasta')
           )
        if File.exist? _
          erev "The file is now available at `#{sfile(_)}`."
        end
      else
        # ================================================================= #
        # The above download_fasta() makes use of NCBI. We need to rewrite
        # this eventually. For now, we will do another, simpler approach
        # here.
        # ================================================================= #
        what = URI.open(i).read
        into = log_dir?+File.basename(i)
        erev "Storing into `#{sfile(into)}#{rev}`."
        write_what_into(what, into)
        return into # This will also return the local path.
      end
    else
      # erev 'Unsure what to do with '+sfancy(i)
      esystem "wget #{i}"
    end
  end
end

#download_fasta(i = nil) ⇒ Object

#

download_fasta

Use this to download a fasta sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10234

def download_fasta(i = nil)
  if i.is_a? Array
    i.each {|entry|
      download_fasta(entry)
    }
  else
    # ===================================================================== #
    # Delegate to a special class here.
    # ===================================================================== #
    stored_here = ::Bioroebe.download_fasta(i) # bl $BIOROEBE/download_fasta.rb
    if stored_here
      if File.exist? stored_here
        assign_sequence(stored_here)
      end
      return stored_here
    else
      e crimson('No result could be found for ')+sfancy(i)+rev
    end
  end
end

#download_this_pdb_file(i = '3O30') ⇒ Object

#

download_this_pdb_file

Use this method to download a .pdb file.

There seem to be at least two major methods how to use the PDB database:

(1) http://www.rcsb.org/pdb/files/3O30.pdb
(2) http://www.rcsb.org/pdb/explore.do?structureId=1QRI

The files/ URI seems to redirect you directly to the .pdb file in question, so I think it is the preferred way. However had, the explore.do query gives additional information.

Other useful URLs are:

http://www.rcsb.org/pdb/explore.do?structureId=1ZAA
http://dx.doi.org/10.2210/pdb1gi5/pdb

Usage example:

download_this_pdb_file http://www.rcsb.org/pdb/files/3O30.pdb
#


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# File 'lib/bioroebe/shell/shell.rb', line 3889

def download_this_pdb_file(
    i = '3O30'
  )
  i = ['3O30'] if i.nil? # If nil, use a default value.
  if i.is_a? Array
    i = ['3O30'] if i.empty?
    i.each {|entry| download_this_pdb_file(entry) }
  else
    i = i.to_s.dup
    unless i.end_with? '.pdb'
      i << '.pdb'
    end
    unless i.start_with? 'http://www.rcsb.org/pdb/files/'
      i[0,0] = 'https://www.rcsb.org/pdb/files/'
    end
    target_dir = download_dir?
    cd target_dir
    # ===================================================================== #
    # http://www.rcsb.org/pdb/files/3O30.pdb
    # ===================================================================== #
    download_this = "#{i.to_s}"
    erev "Checking for the availability of "\
         "#{olivedrab(download_this)}#{rev} next ..."
    if does_this_remote_file_exist?(download_this)
      erev 'Next downloading '+sfancy(download_this)+
           rev+' into '+sfancy(target_dir)+'.'
      esystem "wget #{download_this}" # We will just use wget for now.
      _ = ::Bioroebe.pdb_directory?
      if File.directory? _
        new_target = _+File.basename(download_this)
        erev 'Moving into '+sfancy(new_target)+rev+', where '\
             '.pdb files are kept by default.'
        mv(
          target_dir+File.basename(download_this),
          new_target
        )
      end
      register_this_download(download_this)
    else
      erev "The remote file at #{sfile(download_this)} #{rev}does not exist."
      erev 'Hence, we can not download it.'
    end
  end
end

#dump(optional_arguments = nil) ⇒ Object

#

dump

This method can be used to save the main DNA string into a file.

You can also store RNA of course; simply pass the argument “rna” or “to_rna” to this method.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8608

def dump(
    optional_arguments = nil
  )
  what = dna_string?
  if optional_arguments.is_a? Array
    optional_arguments = optional_arguments.join(' ').strip
  end
  case optional_arguments
  when 'rna',/to_?rna/
    what = ::Bioroebe.to_rna(what)
  end
  into = file_dna_string_saved?
  erev 'Storing into `'+sfile(into)+'`.'
  write_what_into(what, into)
end

#e(i = '') ⇒ Object

#

e (e tag)

#


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# File 'lib/bioroebe/shell/shell.rb', line 955

def e(
    i = ''
  )
  ::Bioroebe.e(i)
  if i and !i.empty?
    set_result(i) # This method will always assign to :result.
  end
end

#ee(i) ⇒ Object

#

ee (ee tag)

As e, but without newline. So basically it behaves like print.

#


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# File 'lib/bioroebe/shell/shell.rb', line 969

def ee(i)
  e(i, false)
end

#efetch(i) ⇒ Object

#

efetch

Invocation example:

efetch https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=189458859&rettype=fasta&retmode=text
#


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# File 'lib/bioroebe/shell/shell.rb', line 1652

def efetch(i)
  if i.is_a? Array
    i.each {|entry| efetch(entry) }
  else
    ::Bioroebe::Ncbi.efetch_by_url(i)
  end
end

#enable(i) ⇒ Object Also known as: use

#

enable (enable tag)

Enable-functionality can be passed through this method here.

Invocation example from within the bioshell:

enable colours
#


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# File 'lib/bioroebe/shell/shell.rb', line 3104

def enable(i)
  if i.is_a? Array
    i = i.join.strip
  end
  case i.to_s # case tag
  # ======================================================================= #
  # === enable cd_aliases
  #
  # This variant will be verbose.
  # ======================================================================= #
  when /^-?-?cd(-|_)?aliases$/
    erev 'class '+
         steelblue('Rcfiles::DirectoryAliases')+rev+' will be '\
         'enabled next, allowing'
    erev 'you to navigate the local filesystem '\
         'more easily so.'
    ::Bioroebe::Configuration.do_use_expand_cd_aliases
  # ======================================================================= #
  # === use colours
  # ======================================================================= #
  when /^colou?rs$/
    enable_colours
  # ======================================================================= #
  # === use xsel
  # ======================================================================= #
  when 'xsel'
    enable_xsel
  end
end

#enable_colours_in_an_extended_manner(be_verbose = :be_quiet) ⇒ Object Also known as: extended_enable_colours

#

enable_colours_in_an_extended_manner (enable tag)

We bundle all colour stuff here. Right now we use only the colour yellow.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10702

def enable_colours_in_an_extended_manner(
    be_verbose = :be_quiet
  )
  enable_colours(be_verbose)
  ::Bioroebe.enable_colours
  set_default_highlight_colour
end

#enable_configuration ⇒ Object

#

enable_configuration

#


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# File 'lib/bioroebe/shell/shell.rb', line 10713

def enable_configuration
  config_dir = ::Bioroebe.project_yaml_directory?+
               '/configuration/'
  unless Object.const_defined?(:Roebe) and
         Roebe.const_defined?(:Configuration)
    begin
      require 'roebe/configuration/class/configuration.rb'
    rescue LoadError; end
  end
  if Object.const_defined?(:Roebe) and
     Roebe.const_defined?(:Configuration)
    # ===================================================================== #
    # === Initialize @configuration
    # ===================================================================== #
    @configuration = ::Roebe::Configuration.new(config_dir, :do_not_run_yet)
    @configuration.be_verbose if @configuration.respond_to? :be_verbose
    @configuration.run
  else
    @configuration = nil
  end
end

#enable_gtk ⇒ Object

#

enable_gtk

This enables gtk.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8477

def enable_gtk
  begin
    if ENV['IS_ROEBE'].to_s
      load_gtk
      # =================================================================== #
      # Pulling in the controller.rb file is enough to also require the
      # other GTK-GUI components of the Bioroebe project.
      # =================================================================== #
      require 'bioroebe/gui/gtk3/controller/controller.rb'
    end
    return ::Bioroebe.controller # This will instantiate a new GTK widget.
  rescue LoadError => error
    e 'Failed to load GTK-related files. Showing the specific error next:'
    pp error
  end
end

#enable_gtk_section_antisensestrand ⇒ Object

#

enable_gtk_section_antisensestrand

#


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# File 'lib/bioroebe/shell/shell.rb', line 8505

def enable_gtk_section_antisensestrand
  require 'bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb'
  e 'Starting AntiSenseStrand ...'
  Bioroebe::GUI::Gtk::AntiSenseStrand.start_gui_application
end

#enable_xsel ⇒ Object

#

enable_xsel

#


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# File 'lib/bioroebe/shell/shell.rb', line 9005

def enable_xsel
  if @internal_hash[:use_xsel]
    e 'xsel is already enabled.'
  else
    e 'Now enabling xsel.'
    @internal_hash[:use_xsel] = true
  end
end

#ensure_that_the_bioshell_log_directory_exists ⇒ Object

#

ensure_that_the_bioshell_log_directory_exists

#


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# File 'lib/bioroebe/shell/shell.rb', line 5228

def ensure_that_the_bioshell_log_directory_exists
  # ======================================================================= #
  # We must check whether we really wish to create directories on startup
  # or not.
  # ======================================================================= #
  if @internal_hash and
     @internal_hash.has_key?(:create_directories_on_startup_of_the_shell) and
     @internal_hash[:create_directories_on_startup_of_the_shell]
    _ = bioshell_log_dir?
    unless File.directory? _
      unless @internal_hash[:silent_startup]
        erev "Next creating the directory #{sdir(_)}#{rev}."
      end
      mkdir(_)
    end
    # ===================================================================== #
    # Determine the path of the .yml file.
    # ===================================================================== #
    yaml_file = ::Bioroebe.project_yaml_directory?+
                'create_these_directories_on_startup/'\
                'create_these_directories_on_startup.yml'
    if File.exist? yaml_file
      YAML.load_file(yaml_file).each {|entry|
        # ================================================================= #
        # Create all specified subdirectories next.
        # ================================================================= #
        _ = "#{log_dir?}#{entry}/"
        unless File.directory? _
          unless @internal_hash[:silent_startup]
            erev "Next creating the directory #{sdir(rds(_))}#{rev}."
          end
          mkdir(_)
        end
      }
    end
  end
end

#enter_base_directory ⇒ Object

#

enter_base_directory

Use this method to enter the base directory.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6114

def enter_base_directory
  cd ::Bioroebe.log_dir?
end

#enter_the_main_loop ⇒ Object Also known as: loop_get_user_input, enter_main_loop

#

enter_the_main_loop (loop tag)

This is the main-loop of the shell.

#


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# File 'lib/bioroebe/shell/shell.rb', line 11543

def enter_the_main_loop
  exit_from_the_main_loop = false
  loop {
    begin
      obtain_user_input                         # 1) Obtain the user input here.
      add_the_current_user_input_to_the_history # 2) Add the user input to the history.
      if @internal_hash[:user_input]
        unless @internal_hash[:user_input].empty?
          # =============================================================== #
          # Pass the user input into the menu next. We will use an
          # Array for this, as user input such as "ls; random 20" should
          # also be valid.
          # =============================================================== #
          user_input = [ @internal_hash[:user_input] ].flatten
          user_input.each {|use_this_as_user_input|
            # ============================================================= #
            # Keep track of the "original" input next:
            # ============================================================= #
            @internal_hash[:original_input] = use_this_as_user_input.dup.chomp.dup
            # ============================================================= #
            # Remove leading 5'- and trailing -3' as these are currently
            # forbidden as input. This check should come quite early.
            #
            # Example input for that may demonstrate this:
            #
            #   5'-ATGGGCAAA
            #
            # ============================================================= #
            use_this_as_user_input[0, 3] = '' if use_this_as_user_input.start_with?("5'-")
            use_this_as_user_input[-3,3] = '' if use_this_as_user_input.end_with?("-3'")
            use_this_as_user_input[-3,3] = '' if use_this_as_user_input.end_with?("-'3")
            # ======================================================================= #
            # === Handle special arguments next
            #
            # Must not start and end with a number, as we will assume input such
            # as "11 - 33" in this case. However had, input such as "random 333"
            # must remain valid.
            #
            # Note that the following input may also be valid:
            #
            #   3to1 ARG-ALA-SER-LEU-PHE-TRP-LYS-HIS-ASN-SER-VAL-LEU-ILE-VAL-PRO
            #
            # This explains why the Regex is a bit complicated.
            # ======================================================================= #
            if use_this_as_user_input.include?(' ') and
              (use_this_as_user_input !~ /^\d+\s+/) and
              (use_this_as_user_input !~ /^\d+.+\d{1,3}\s+$/)
              # ===================================================================== #
              # We must keep in mind that input may be an assignment too,
              # sometimes. In these cases the input will include a '='
              # character. But it could also be an assignment towards
              # a sequence, such as in the following case:
              #
              #   [33,0] = GAATTC
              #
              # ===================================================================== #
              case use_this_as_user_input
              # ===================================================================== #
              # === Assignment via [START_POSITION, END_POSITION]
              #
              # This is a shortcut that allows us to quickly grab a subsequence.
              #
              # See the following link for the explanation of the regex:
              #
              #   https://rubular.com/r/J13Eikdly0
              #
              # Usage example:
              #
              #   [33,0] = GAATTC
              #
              # ===================================================================== #
              when /^\[?(\d{0,10}),\s{0,1}(\d{0,10})\]?\s*=\s*'?([A-Za-z]*)'?$/
                start_position = $1.to_s.dup
                end_position   = $2.to_s.dup
                new_string     = $3.to_s.dup
                erev simp(new_string.size.to_s)+rev+' nucleotides will be inserted '\
                     'at nucleotide position '+
                     sfancy(start_position.to_s)+rev+'.'
                dna_sequence_object?[start_position, end_position] = new_string
                return # Do not evaluate any further for this entry point.
              # ===================================================================== #
              # === User may try a comparison such as:
              #
              #   ATCGATCGATCG == ATCGATCG
              #   ATG == ATG
              #
              # ===================================================================== #
              when /==/
                erev try_to_compare_these_two_sequences_for_equality(use_this_as_user_input)
                return # And "exit" here.
              end
            end
            # ======================================================================= #
            # === Chop off "?" if it is the last character
            # ======================================================================= #
            if use_this_as_user_input.end_with?('?') and (use_this_as_user_input.size > 1)
              if debug?
                ewarn 'Removing the last character `?` in order to '\
                      'simplify input handling.'
              end
              use_this_as_user_input.chop!
            end if remove_question_mark?
            # ======================================================================= #
            # Next check for three-letter code as input.
            # ======================================================================= #
            if use_this_as_user_input.include?('-') and
               Bioroebe.is_in_the_three_letter_code?(use_this_as_user_input)
              erev 'A three-letter aminoacid sequence was given as input.'
              erev 'This will be changed into the most likely aminoacid'
              erev 'sequence.'
              use_this_as_user_input = Bioroebe.deduce_most_likely_aminoacid_sequence_as_string(
                    Bioroebe.three_to_one(
                      use_this_as_user_input.delete('-')
                    )
                  )
              assign(use_this_as_user_input) { :be_verbose }
            end
            parse_this_user_input(use_this_as_user_input) # 3) Always parse the user input.
            # ============================================================= #
            # Intercept " quotes here.
            # ============================================================= #
            if use_this_as_user_input.include?('"') and use_this_as_user_input.include?(N)
              # a = start_clipboard('"') if i.include? '"'
              start_clipboard('"') if use_this_as_user_input.include? '"'
            end
            result_from_the_menu = menu(
              @internal_hash[:command_to_be_passed_to_the_menu]
            )
            case result_from_the_menu
            # ============================================================= #
            # === :exit_gracefully
            # ============================================================= #
            when :exit_gracefully
              say_goodbye
              exit_from_the_main_loop = true
            # ============================================================= #
            # === :break
            # ============================================================= #
            when :break
              case exit_the_shell_how?
              # =========================================================== #
              # === :exit_gracefully
              # =========================================================== #
              when :exit_gracefully # User wants to exit here.
                say_goodbye
                exit_from_the_main_loop = true
              # =========================================================== #
              # === :instantly
              # =========================================================== #
              when :instantly
                exit_from_the_main_loop = true
              end
              exit_from_the_main_loop = true
            else
            end
          }
          @internal_hash[:user_input] = nil # And clear it here again.
        end
      end
      if exit_from_the_main_loop == true
        break
      end
    # ===================================================================== #
    # Rescue sigints (aka ctrl-c) and SystemExit.
    # ===================================================================== #
    rescue Interrupt, SystemExit
      e
    end
  }
end

#ereturn(i = '') ⇒ Object

#

ereturn

#


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# File 'lib/bioroebe/shell/shell.rb', line 6287

def ereturn(i = '')
  e i
  return
end

#erev(i = '') ⇒ Object

#

erev (erev tag)

Easier wrapper over output that has rev().

#


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# File 'lib/bioroebe/shell/shell.rb', line 9247

def erev(i = '')
  e "#{rev}#{i}"
end

#exit_the_shell_how? ⇒ Boolean

#

exit_the_shell_how?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 1059

def exit_the_shell_how?
  @internal_hash[:exit_the_shell_how]
end

#extract_sequence_from_this_file(i) ⇒ Object Also known as: extract_sequence

#

extract_sequence_from_this_file

Use this method to extract a DNA sequence from the given file.

The given input should thus, logically, be an existing (local) file.

Currently this works via genbank .gb files but in the future, other formats may well be supported too.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8944

def extract_sequence_from_this_file(i)
  if i.is_a? Array
    i.each {|entry| extract_sequence_from_this_file(entry) }
  else
    if File.exist? i
      extname = File.extname(i).delete('.')
      case extname
      when 'gb'
        # =================================================================== #
        # Handle genbank .gb files here.
        # =================================================================== #
        _ = ::Bioroebe::GenbankParser.new(i) { :do_not_report_anything }
        assign_sequence(_.sequence?)
      end
    else
      no_file_exists_at(i)
    end
  end
end

#fasta? ⇒ Boolean Also known as: last_fasta?, last_fasta_entry?

#

fasta?

We need a query method over the main fasta object, IF it was set.

Since we already have an Array that keeps track of these objects, we can simply grab the last one from that collection.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 3664

def fasta?
  array_fasta?.last
end

#fasta_file?(i = :fasta_file) ⇒ Boolean

#

fasta_file?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6054

def fasta_file?(i = :fasta_file)
  if @internal_hash[:fasta_file].has_key?(i)
    @internal_hash[:fasta_file].fetch(i)
  else
    erev 'We could not find the key called `'+simp(i.to_s)+rev+'`.'
  end
end

#feedback_version ⇒ Object

#

feedback_version

#


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# File 'lib/bioroebe/shell/shell.rb', line 7560

def feedback_version
  erev version?
end

#feedback_where_files_are_kept_locally ⇒ Object

#

feedback_where_files_are_kept_locally

We feedback where some files are kept, like the restriction enzymes.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8116

def feedback_where_files_are_kept_locally
  erev 'The restriction enzymes are kept here:'
  e
  e "  #{sfile(::Bioroebe.restriction_enzymes_file)}"
  e
  erev 'The files with the mass table of the amino acids is kept here:'
  e
  e "  #{sfile(::Bioroebe::FILE_AMINO_ACIDS_MASS_TABLE)}"
  e
  report_where_we_store
end

#feedback_whether_we_are_in_debug_mode ⇒ Object

#

feedback_whether_we_are_in_debug_mode

#


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# File 'lib/bioroebe/shell/shell.rb', line 10766

def feedback_whether_we_are_in_debug_mode
  erev 'Are we in debug mode? '+simp(debug?.to_s)+rev
end

#feedback_whether_we_will_also_set_the_xorg_buffer ⇒ Object

#

feedback_whether_we_will_also_set_the_xorg_buffer

#


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# File 'lib/bioroebe/shell/shell.rb', line 8701

def feedback_whether_we_will_also_set_the_xorg_buffer
  erev "Will we also set the Xorg buffer? "\
       "#{sfancy(vt(configuration?.additionally_set_xorg_buffer.to_s))}"
end

#fetch_from_pdb(i) ⇒ Object

#

fetch_from_pdb

This method can obtain a .pdb file from the pdb website.

It can also return the aminoacid sequence.

A URL for the .pdb may be available like this:

https://files.rcsb.org/view/2BTS.pdb
https://files.rcsb.org/view/355D.pdb

For the FASTA sequence, try:

https://www.rcsb.org/fasta/entry/2BTS/display
#


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# File 'lib/bioroebe/shell/shell.rb', line 5760

def fetch_from_pdb(i)
  if i.is_a? Array
    i = i.join(' ').strip
  end
  i.upcase!
  remote_url = "https://www.rcsb.org/structure/#{i}"
  erev 'Looking for the protein called '+steelblue(i)+rev+
       ' at pdb next. (URL: '+royalblue(remote_url)+rev+')'
  e
  open_in_browser(remote_url)
  e
  remote_url_to_the_pdb_file = "https://files.rcsb.org/view/#{i}.pdb"
  esystem "wget #{remote_url_to_the_pdb_file}"
  e
  begin
    erev 'The fasta sequence, obtained from '+remote_url+', is:'
    e
    result = ::Bioroebe.return_fasta_sequence_from_this_pdb_file(remote_url)
    e result
    e
    set_aminoacid_sequence(result) # And assign it as well.
  rescue Exception => error
    pp error
  end
  # ======================================================================= #
  # The file may be without a .pdb entry, so rename it in that case.
  # ======================================================================= #
  target = File.basename(remote_url_to_the_pdb_file)
  if File.exist? target
    unless target.end_with? '.pdb'
      unless File.exist? target+'.pdb'
        new_location = target
        rename_file(i, new_location) unless File.exist?(new_location)
        target = new_location
      end
    end
    move_file_to_its_correct_location(target)
  end
end

#file_dna_string_saved? ⇒ Boolean

#

file_dna_string_saved?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 10801

def file_dna_string_saved?
  @internal_hash[:file_dna_string_saved]
end

#find_all_orfs(i = dna_sequence? ) ⇒ Object

#

find_all_orfs

This method will return all ORFs within the target sequence.

It will return an Array, and then we will display these ORFs, starting with the LONGEST ORF first.

#


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# File 'lib/bioroebe/shell/shell.rb', line 11043

def find_all_orfs(
    i = dna_sequence?
  )
  all_start_codons = i.to_enum(:scan, /#{::Bioroebe.start_codon?}/i).map { |match|
    [$`.size] # [$`.size, match]
  }
  all_stop_codons = i.to_enum(:scan, /(TGA|TAG|TAA)/i).map { |match|
    [$`.size]
  }
  array_with_the_proper_matches = []
  current_match = nil
  all_start_codons.each {|start_codon_position|
    start_codon_position = start_codon_position.first
    # ===================================================================== #
    # Find the nearest stop codon position.
    # ===================================================================== #
    all_stop_codons.reverse.each {|stop_codon_position|
      stop_codon_position = stop_codon_position.first
      length = stop_codon_position - start_codon_position
      next if length < 1
      current_match = [start_codon_position, length]
      if current_match
        # Must be a smaller match.
        if length < current_match[1] # [1] refers to the length.
          unless length < 3
            current_match = [start_codon_position, length]
          end
        end 
      end
    }
    array_with_the_proper_matches << current_match
  }
  cliner token: '-'
  pp array_with_the_proper_matches
  cliner token: '-'
  _ = dna_sequence?
  array_with_the_proper_matches.each {|start, stop|
    subsequence = _[start.to_i .. stop.to_i]
    erev subsequence unless subsequence.empty?
  }
end

#find_complementary_strand(i = dna_sequence? ) ⇒ Object Also known as: show_complementary_strand

#

find_complementary_strand

Invoke this via:

3'-ATGCCTGCC
#


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# File 'lib/bioroebe/shell/shell.rb', line 11879

def find_complementary_strand(
    i = dna_sequence?
  )
  _ = i.strip # The original input.
  if _.include? "3'-" and _.start_with?('3')
    _.gsub!(/3'-/,'')
    _.gsub!(/-5'/,'')
    _.gsub!(/3'-/,'')
    erev lpad?+leading_three_prime+
         colourize_nucleotide(_, :do_not_add_anything_else)+
         trailing_five_prime
  end
  result = lpad?+
           colourize_nucleotide(
             return_complement(i.reverse)
           )
  erev result
  return result
end

#find_gene(i = :default) ⇒ Object

#

find_gene

Wrapper towards class Bioroebe::FindGene.

#


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# File 'lib/bioroebe/shell/shell.rb', line 11185

def find_gene(i = :default)
  case i
  when :default, nil
    i = dna_sequence?
  end 
  if i.empty?
    report_that_a_string_must_be_assigned_first
  else
    ::Bioroebe::FindGene.new(i.upcase) # bl $BIOROEBE/find_gene.rb
  end
end

#find_kdel_sequence ⇒ Object

#

find_kdel_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 4570

def find_kdel_sequence
  # ======================================================================= #
  # We must operate on the aminoacid-sequence next.
  # ======================================================================= #
  aminoacid_sequence = aminoacid_sequence?.to_s
  scan_result = aminoacid_sequence.scan(/KDEL/)
  has_kdel = scan_result.empty?
  if has_kdel
    erev 'This sequence has at the least '+
         steelblue('one')+' KDEL sequence. '\
         '(Has '+scan_result.size.to_s+')'
  else
    erev 'This sequence does not have any KDEL sequence.'
  end
end

#find_longest_substring(i = dna_string?) ) ⇒ Object

#

find_longest_substring

#


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# File 'lib/bioroebe/shell/shell.rb', line 6207

def find_longest_substring(i = dna_string?)
  if i.is_a? String and i.include? ' '
    i = i.split(' ')
  end
  ::Bioroebe::FindLongestSubstring.new(i.first, i.last)
end

#find_longest_substring_via_LCS(i) ⇒ Object

#

find_longest_substring_via_LCS

To invoke this, try:

longest_substring? ATTATTGTT | ATTATTCTT
#


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# File 'lib/bioroebe/shell/shell.rb', line 7777

def find_longest_substring_via_LCS(i)
  i = i.join(' | ') if i.is_a? Array
  ::Bioroebe::FindLongestSubstringViaLCSalgorithm.new(i) { :do_also_show_the_two_sequences }
end

#find_restriction_enzymes_that_cut_at(i) ⇒ Object

#

find_restriction_enzymes_that_cut_at

A wrapper over find_restriction_sites().

#


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# File 'lib/bioroebe/shell/shell.rb', line 9037

def find_restriction_enzymes_that_cut_at(i)
  erev 'Trying to find restriction enzymes that '\
       'cut at `'+sfancy(i)+rev+'`.'
  result = find_restriction_sites(i)
  unless result
    erev 'Found no result for this sequence.'
  end
end

#find_restriction_sites(i = string?) ) ⇒ Object

#

find_restriction_sites

Call the parent method in the Bioroebe class.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8230

def find_restriction_sites(i = string?)
  i = string? if i.nil?
  Bioroebe.restriction_sites?(i) # bl mybioruby
end

#find_shine_dalgarno_sequence(i = dna_sequence_as_string? ) ⇒ Object

#

find_shine_dalgarno_sequence

Use this method to attempt to try and find a SD-sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3286

def find_shine_dalgarno_sequence(
    i = dna_sequence_as_string?
  )
  i.upcase! # Need to ensure upcased input.
  pure_sd_sequence = 'AGGAGGU'.dup
  if is_dna?
    pure_sd_sequence.tr!('U','T')
  end
  if i.nil?
    report_that_a_string_must_be_assigned_first
  else
    sd_sequence = steelblue(
      dna_padding(pure_sd_sequence, :no_spaces).lstrip
    )
    if i.include? 'T' # Assume that we have a DNA string rather than RNA.
      pure_sd_sequence = 'AGGAGGT'
      sd_sequence = steelblue(
        dna_padding(pure_sd_sequence, :no_spaces).lstrip
      )
    end
    if i.include? pure_sd_sequence
      erev "Yes, our string contains at least one Shine Dalgarno "\
           "(#{sd_sequence}#{rev}) sequence."
      n_sd_sequences = i.scan(/#{pure_sd_sequence}/).size.to_s
      erev 'We have found '+sfancy(n_sd_sequences)+rev+' instance(s) of '\
           'Shine Dalgarno ('+sd_sequence+rev+') Sites.'
      erev 'We will next show the particular sequence in '\
           'question ('+simp(pure_sd_sequence)+rev+').'
      # =================================================================== #
      # Next, try to find restriction enzymes that cut at the
      # Shine-Dalgarno site.
      # =================================================================== #
      try_to_find_restriction_enzymes_for(:shine_dalgarno)
    else
      erev "We did not find a Shine Dalgarno ("\
           "#{simp(sd_sequence)}#{rev}) sequence."
    end
  end
end

#first(i) ⇒ Object

#

first

#


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# File 'lib/bioroebe/shell/shell.rb', line 7069

def first(i)
  if i.to_s =~ /^\d+$/ # If the input is only numbers
    erev 'Obtaining the first '+simp(i).to_s+rev+' nucleotides next:'
    erev simp(seq?[0,i.to_i])
  else # Else change the first nucleotide.
    change_first_nucleotide_to(f)
  end
end

#first_argument? ⇒ Boolean Also known as: f?, f

#

first_argument?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7438

def first_argument?
  @internal_hash[:first_argument]
end

#format_this_nucleotide_sequence(i, &block) ⇒ Object

#

format_this_nucleotide_sequence

This method will properly format the passed-in nucleotide sequence, by making use of class ShowNucleotideSequence.

It will return the formatted String.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6105

def format_this_nucleotide_sequence(i, &block)
  ::Bioroebe.format_this_nucleotide_sequence(i) { block }
end

#freeze_the_main_sequence ⇒ Object

#

freeze_the_main_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 5359

def freeze_the_main_sequence
  @internal_hash[:the_main_sequence_is_frozen] = true
end

#generate_palindrome(i) ⇒ Object

#

generate_palindrome

This method will generate a Palindrome sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3642

def generate_palindrome(i)
  i = i.join.strip if i.is_a? Array
  ::Bioroebe::PalindromeGenerator.new(i).report
end

#generate_pdf_tutorial ⇒ Object

#

generate_pdf_tutorial

Easier wrapper to generate the .pdf Tutorial.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5983

def generate_pdf_tutorial
  ::Bioroebe.generate_pdf_tutorial
end

#generate_random_dna_sequence_with_variable_length_and_variable_composition ⇒ Object

#

generate_random_dna_sequence_with_variable_length_and_variable_composition

This method will generate a random DNA sequence of variable length and composition.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2836

def generate_random_dna_sequence_with_variable_length_and_variable_composition
  e 'Input the desired length of your DNA string:'
  length = $stdin.gets.chomp.to_i
  e 'Input the percentage of Adenine, Thymin, Cytosine and Guanosine. You can'
  e 'omit this, in which case we will default to 25% each.'
  e 'Use a / as delimiter please, as in '+
    orange('30 / 30 / 20 / 20')+rev+'.'
  e
  print 'Adenine / Thymin / Cytosine / Guanosine: '
  composition = $stdin.gets.chomp
  if composition.include? '/'
    splitted = composition.split('/').
               map(&:strip).map(&:to_f)
  else
    splitted = [25,25,25,25]
  end
  # ======================================================================= #
  # Next, we fill in our pool of nucleotides.
  # ======================================================================= #
  pool_of_nucleotides = []
  # ======================================================================= #
  # Next, we must determine how many we will use. The percentage value
  # tells us this.
  # The entries are e. g. 35%. So we first must calculate how much is
  # 1%, then we multiply this.
  # ======================================================================= #
  n_A = (length.to_f / 100) * splitted[0].to_f
  n_T = (length.to_f / 100) * splitted[1].to_f
  n_C = (length.to_f / 100) * splitted[2].to_f
  n_G = (length.to_f / 100) * splitted[3].to_f
  pool_of_nucleotides << (['A'] * n_A)
  pool_of_nucleotides << (['T'] * n_T)
  pool_of_nucleotides << (['C'] * n_C)
  pool_of_nucleotides << (['G'] * n_G)
  pool_of_nucleotides.flatten!
  _ = ''.dup # This is the return string.
  _ << pool_of_nucleotides.shuffle.join
  return _
end

#generate_random_protein_sequence_with_variable_length_and_variable_composition ⇒ Object

#

generate_random_protein_sequence_with_variable_length_and_variable_composition

Use this method to generate a random protein sequence with variable length and variable composition.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7600

def generate_random_protein_sequence_with_variable_length_and_variable_composition
  _ = {} # This is our hash.
  e 'You can generate a random protein sequence next. First, input the'
  print 'target length of the protein in question: '
  length = $stdin.gets.chomp.to_i
  e
  e 'Next, you have to input the percentage for the respective amino '\
    'acids, separated via the token '+orange('/')+rev+'.'
  e
  e 'This can be quite tedious though. Unfortunately, there is not a'
  e 'much simpler way possible on the commandline, so here we go:'
  e
  print 'Glycine Alanine Valine: '
  glycine_alanine_valine   = $stdin.gets.chomp
  glycine, alanine, valine = glycine_alanine_valine.split('/').map(&:strip)
  _['glycine'] = glycine
  _['alanine'] = alanine
  _['valine'] = valine
  e 'The length of the target protein is '+simp(length.to_s)+'.'
e swarn('!!! THE ABOVE CODE ^^^ IS UNFINISHED !!!!!')+rev
end

#generate_single_sequence_repeats ⇒ Object

#

generate_single_sequence_repeats

This method can be used to generate SSR sequences.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5582

def generate_single_sequence_repeats
  _ = ''.dup
  length_of_the_SSR_sequence = 2+rand(4) # 2-5
  length_of_the_SSR_sequence.times {
    _ << return_random_nucleotide
  }
  n_repeats = 9+rand(22) # 9-30
  result = _ * n_repeats
  return result
end

#get_long_name_of_amino_acid(i) ⇒ Object

#

get_long_name_of_amino_acid

#


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# File 'lib/bioroebe/shell/shell.rb', line 5865

def get_long_name_of_amino_acid(i)
  amino_acids_table = AMINO_ACIDS
  if amino_acids_table.has_key? i
    _ = amino_acids_table[i]
    key = _.keys.select {|inner_key| inner_key.size == 3 }[0]
    i = _[key].to_s
  end
  return i
end

#guanin? ⇒ Boolean

#

guanin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 10137

def guanin?
  YAML.load_file(FILE_NUCLEOTIDES)['Guanin']
end

#handle_fasta(i) ⇒ Object Also known as: assign_fasta, handle_this_fasta_file

#

handle_fasta

Use this method to properly handle a fasta file.

The argument should be the (local) path to a fasta file.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4349

def handle_fasta(i)
  if i.nil?
    if File.exist? fasta_file?.to_s
      e sfile(fasta_file?.to_s)
    else
      show_my_fasta_file # As a reminder.
    end
  else
    i = i.to_s unless i.is_a? String # Need a String past this point.
    if File.exist?(i) and i.end_with?('.fasta')
      opnerev 'Trying to parse the file `'+sfile(i)+rev+'` next.'
      parse_fasta_format(i)
    else
      fasta_files = Dir['*.fasta']
      unless fasta_files.empty?
        erev 'There seems to be at least one .fasta file in this '\
             'directory ('+sdir(return_pwd)+').'
      end
    end
  end
end

#handle_pdb_files(i) ⇒ Object

#

handle_pdb_files

This method will either show more information about .pdb files or it will simply attempt to download the .pdb file in question.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1666

def handle_pdb_files(i)
  if i.nil? or i.empty?
    # In this case, we show some info.
    cliner
    erev '.pdb files are files in the "Protein Data Bank" format.'
    e
    erev 'It is a standard for files containing atomic coordinates.'
    e
    erev 'Each line in a .pdb file is called a "record".'
    e
    erev 'You can pass an ID (a number) and we will attempt to download '\
         'that .pdb file.'
    e
    erev 'Example:'
    e
    erev '  pdb 333'
    e
    erev 'More information can be seen here:'
    e
    efancy '  https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html'
    e
    print rev
    cliner
  else
    download_this_pdb_file(i)
  end
end

#handle_this_file(this_file) ⇒ Object

#

handle_this_file

This method can be used to handle a file in general.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4014

def handle_this_file(this_file)
  if File.exist?
    e File.read(this_file)
  end
end

#highlight_colour? ⇒ Boolean Also known as: yellow

#

highlight_colour?

The highlight colour is primarily the colour that we will use on the commandline, for instance, to denote pretty colours.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 9579

def highlight_colour?
  @highlight_colour
end

#identify_aminoacid(i) ⇒ Object

#

identify_aminoacid

This method will also display the long name of the aminoacid at hand.

Note that you can also identify a batch of aminoacids, by using the ‘-’ character.

Example for this:

identify_aminoacid A-Z

We will ignore invalid aminoacids though.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8734

def identify_aminoacid(i)
  if i.is_a? Array
    i.flatten!
    if i.any? {|inner_entry| inner_entry.include? '-'}
      # =================================================================== #
      # In this case, at the least one entry has a '-' Range component.
      # So we must substitute there.
      # =================================================================== #
      i.map! {|most_inner_entry|
        if most_inner_entry.include?('-')
          # =============================================================== #
          # Assume a Range in this case and prepare it accordingly.
          # =============================================================== #
          chars = most_inner_entry.chars
          start_position = chars.first
          end_position   = chars.last
          most_inner_entry = (start_position .. end_position).to_a
          most_inner_entry = strict_filter_away_invalid_aminoacids(most_inner_entry)
          most_inner_entry
        end
        most_inner_entry
      }
    end
    # ===================================================================== #
    # Recursively call the method if the input is an Array.
    # ===================================================================== #
    i.flatten!
    e; i.each {|entry|
      identify_aminoacid(entry)
    }; e
  else # else assume a String.
    _ = ::Bioroebe::AMINO_ACIDS_MASS_TABLE
    if i.empty?
      erev 'Please supply at the least one character '\
           '(aminoacid one letter code).'
    elsif _.has_key? i
      long_name_of_the_aminoacid = FILE_AMINO_ACIDS_ENGLISH[i]
      erev i.ljust(3)+' ('+sfancy(long_name_of_the_aminoacid)+
           rev+') corresponds to a molecular weight of '+
           simp(_[i])+rev+' Dalton.'
    else
      erev "Did not find `#{simp(i)}`."
    end
  end
end

#include?(i) ⇒ Boolean

#

include?

This can be used to check if we include a string or not.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 3939

def include?(i)
  _ = dna_string?
  if _
    if _.include? i
      erev 'Yes, we found it. It is at:'
      pp _.scan(/#{i}/)
    else
      erev 'No, we did not find it.'
    end
  else
    erev 'It seems as if you yet have not defined a main string.'
    erev 'Please do so first, via assign() or random().'
  end
end

#index_this_fasta_file(i) ⇒ Object

#

index_this_fasta_file

This will index FASTA files (.fa or .fasta) via the samtools.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9184

def index_this_fasta_file(i)
  # ======================================================================= #
  # === Handle blocks first
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    when :use_all_fasta_files_if_no_argument_was_given
      if i.nil? or i.empty?
        i = Dir['*.fasta']+
            Dir['*.fa'].flatten.compact
      end
    end
  end
  if i.is_a? Array
    i.each {|entry| index_this_fasta_file(entry) }
  else
    i = i.to_s # Need to work on a String past this point.
    if File.exist? i
      erev "Indexing the following file next, via "\
           "#{steelblue('samtools')}#{rev}:"
      Bioroebe.index_this_fasta_file(i)
    else
      no_file_exists_at(i)
    end
  end
end

#initialize_clipboard ⇒ Object

#

initialize_clipboard

#


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# File 'lib/bioroebe/shell/shell.rb', line 7149

def initialize_clipboard
  begin
    require 'roebe/classes/clipboard.rb'
  rescue LoadError; end
  if Object.const_defined?(:Roebe) and
     Roebe.const_defined?(:Clipboard)
    @internal_hash[:clipboard] = Roebe::Clipboard.new
  else
    @internal_hash[:clipboard] = nil
  end
end

#initialize_main_sequence(n_nucleotides = 250) ⇒ Object Also known as: reset_string

#

initialize_main_sequence

Initialize a Sequence-object on startup. We use the length 150 for now.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8350

def initialize_main_sequence(n_nucleotides = 250)
  sequence_object = Bioroebe::Sequence.new(n_nucleotides)
  # ======================================================================= #
  # Add support for some methods, such as "to_rna":
  # ======================================================================= #
  sequence_object.automatic_support_for_nucleotides
  @internal_hash[:array_dna_sequences] << sequence_object
end

#initialize_the_user_input_specific_variables ⇒ Object

#

initialize_the_user_input_specific_variables

#


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# File 'lib/bioroebe/shell/shell.rb', line 7402

def initialize_the_user_input_specific_variables
  # ======================================================================= #
  # === :all_arguments
  #
  # This variable will hold all arguments given by the user.
  # ======================================================================= #
  @internal_hash[:all_arguments] = []
  # ======================================================================= #
  # === :remaining_arguments
  # ======================================================================= #
  @internal_hash[:remaining_arguments] = []
  # ======================================================================= #
  # === :first_argument
  #
  # This variable refers to the first argument passed into a method,
  # from the menu.rb file.
  # ======================================================================= #
  @internal_hash[:first_argument] = nil
  # ======================================================================= #
  # === :command_to_be_passed_to_the_menu
  #
  # This is the command that will be passed into menu().
  # ======================================================================= #
  @internal_hash[:command_to_be_passed_to_the_menu] = nil
end

#install(i) ⇒ Object

#

install (install tag)

#


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# File 'lib/bioroebe/shell/shell.rb', line 1697

def install(i)
  case i.to_s
  when 'bioruby',
       'bioroebe',
       'bio',
       '1', # install bioroebe.
       :default
    erev 'We now install Bioruby.'
    file_location = '/home/x/src/bioruby/bioruby-2.0.0.tar.xz'
    begin
      Easycompile::Easycompile.new(file_location) # Make use of Easycompile to install it.
    rescue Exception => error
      pp error
    end
  else
    ewarn "Do not know how to install `#{simp(i)}`."
  end
end

#interactive_colour_menu ⇒ Object

#

interactive_colour_menu

#


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# File 'lib/bioroebe/shell/shell.rb', line 8865

def interactive_colour_menu
  erev 'You can decide here whether you want to use colours or not, and if'
  erev 'you want to use colours, whether these will be simple ansi colours'
  erev 'or the "more advanced" konsole submodule of the colours project.'
  e
  erev '  (1) no colours'
  erev '  (2) ansi colours'
  erev '  (3) konsole colours'
  e
  print 'Input your choice next: '
  user_input = $stdin.gets.chomp
  case user_input
  # === 1
  when '1'
    erev 'We will use no colours.'
    disable_colours
  # === 2
  when '2'
    erev 'We will use ansi colours.'
    enable_colours unless use_colours?
    Shell.set_colour(:AnsiColours)
  # === 3
  when '3'
    erev 'We will use konsole colours.'
    enable_colours unless use_colours?
    Shell.set_colour(:Konsole)
  end
end

#interactive_use_of_levensthein(i = all_arguments? ) ⇒ Object

#

interactive_use_of_levensthein

#


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# File 'lib/bioroebe/shell/shell.rb', line 4261

def interactive_use_of_levensthein(
    i = all_arguments?
  )
  require 'bioroebe/string_matching/levensthein.rb'
  erev 'You want to use class '+steelblue('Bioroebe::Levensthein')+
        rev+'. This class needs two'
  erev 'input sequences (defaulting to nucleotides).'
  e
  if i.nil? or i.empty?
    erev 'Input the nucleotide sequence to the '+
         slateblue('first')+rev+' sequence:'
    print '  '; sequence1 = $stdin.gets.chomp
    e
    erev 'Input the nucleotide sequence to the '+
         slateblue('second')+rev+' sequence:'
    print '  '; 
    sequence2 = $stdin.gets.chomp
    ::Bioroebe::Levensthein.new(sequence1, sequence2)
  else
    ::Bioroebe::Levensthein.new(i)
  end
end

#interactively_pick_colour ⇒ Object

#

interactively_pick_colour

This method can be used to interactively assign a new colour for the rev() part.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8276

def interactively_pick_colour
  erev 'You can pick a Konsole colour here, for rev(), which is '\
       'the default colour.'
  erev 'In order to make it a bit easier for you, we will show 5 '\
       'random examples for this:'
  string = ''.dup
  5.times {
    string << ::Colours.colours.sample << ', '
  }
  erev "  #{string}"
  erev 'Input your Colours colour next:'
  user_input = $stdin.gets.chomp
  colour_to_use = ::Colours.send(user_input.to_sym)
  erev colour_to_use+'Testing: '+rev
  # ======================================================================= #
  # Next, set a new default colour to use.
  # ======================================================================= #
  ::Bioroebe.set_default_colour(colour_to_use)
end

#is_a_registered_compound?(i) ⇒ Boolean

#

is_a_registered_compound?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6200

def is_a_registered_compound?(i)
  %w( glycine ).include? i.to_s.downcase
end

#is_a_stop_codon?(i) ⇒ Boolean

#

is_a_stop_codon?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 4172

def is_a_stop_codon?(i)
  ::Bioroebe.is_a_stop_codon?(i)
end

#is_any_nucleotide_assigned? ⇒ Boolean

#

is_any_nucleotide_assigned?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8369

def is_any_nucleotide_assigned?
  !sequence_object?.empty? # If the sequence is not empty, it is assigned.
end

#is_dna? ⇒ Boolean

#

is_dna?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 10867

def is_dna?
  mode? == :dna
end

#is_palindrome?(i) ⇒ Boolean

#

is_palindrome?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7625

def is_palindrome?(i)
  erev ::Bioroebe.is_palindrome?(i) # is_palindrome? GATC
end

#is_the_main_sequence_frozen? ⇒ Boolean Also known as: the_main_sequence_is_frozen?

#

is_the_main_sequence_frozen?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 5373

def is_the_main_sequence_frozen?
  @internal_hash[:the_main_sequence_is_frozen]
end

#is_this_a_cd_alias?(i) ⇒ Boolean

#

is_this_a_cd_alias?

The reason why this does a check for :Rcfiles is because not every user may have the rcfiles-project available.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7512

def is_this_a_cd_alias?(i)
  Object.const_defined?(:Rcfiles) and
  ::Rcfiles::DirectoryAliases.is_this_input_a_cd_alias?(i)
end

#is_this_a_valid_codon?(i) ⇒ Boolean

#

is_this_a_valid_codon?

This method can determine whether the given input is a valid codon or whether it is not.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6307

def is_this_a_valid_codon?(i)
  ::Bioroebe.is_this_a_valid_codon?(i)
end

#last_inputted_command?(array_history = array_history? ) ⇒ Boolean

#

last_inputted_command?

This method will return the last user-inputted element.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 5154

def last_inputted_command?(
    array_history = array_history?
  )
  if array_history and array_history.respond_to?(:last)
    return array_history.last
  end
end

#leading_3_prime ⇒ Object Also known as: leading_three_prime, leading_3

#

leading_3_prime

This is when 3’ is at the start of an output.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8052

def leading_3_prime
  "3' - "
end

#leading_5_prime(get_rid_of_spaces = false) ⇒ Object Also known as: five_prime, leading_five_prime, leader, lead_five_prime, return_five_prime_header, leading_five, five_leader?

#

leading_5_prime

This method will output the leading 5’ part, like a header.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6165

def leading_5_prime(
    get_rid_of_spaces = false
  )
  if show_the_leader?
    get_rid_of_spaces = true if get_rid_of_spaces == :no_spaces
    _ = "5' - ".dup # <- This here is the header-tag.
    _.delete!(' ') if get_rid_of_spaces
    return _
  end
  return ''
end

#left_chop(i) ⇒ Object

#

left_chop

#


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# File 'lib/bioroebe/shell/shell.rb', line 10478

def left_chop(i)
  chop(i, :left)
end

#list(i = nil) ⇒ Object

#

list

#


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# File 'lib/bioroebe/shell/shell.rb', line 3972

def list(i = nil)
  case i
  # ======================================================================= #
  # === list ages
  # ======================================================================= #
  when /^age/
    erev 'We will next list the maximum age of different organisms.'
    if File.exist? BIO_LANG
      hash_results = {}
      dataset = File.read(BIO_LANG)
      n_entries = dataset.scan(/  max_age: /).count
      name_of_organism = ''
      dataset.split(N).each {|line|
        next if line.start_with? '#'
        next if line.empty?
        unless line.start_with?(' ')
          name_of_organism = line.delete(':').strip
        end
        if line.include? '  max_age: '
          its_max_age = line.gsub(/max_age:/,'').strip
          if its_max_age.include? '#'
            its_max_age = its_max_age[0, its_max_age.index('#')]
          end
          its_max_age.strip!
          its_max_age << ' years' unless its_max_age.end_with? 'years'
          hash_results[name_of_organism] = its_max_age
        end
      }
      erev 'We did find '+sfancy(n_entries.to_s)+' results.'
      e
      hash_results.sort_by {|value, key| key }.reverse.each { |name, age|
        erev '  '+(name+':').ljust(30)+' '+sfancy(age.rjust(12))
      }; e # Trailing newline looks nice.
    end
  end
end

#load(i = file_dna_string_saved? ) ⇒ Object Also known as: load_dataset_from

#

load (load tag)

This method will try to load from the given input, if this is an existing file.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4119

def load(
    i = file_dna_string_saved?
  )
  if i.nil?
    load(file_dna_string_saved?)
  # ======================================================================= #
  # === Handle Arrays
  # ======================================================================= #
  elsif i.is_a? Array
    if i.nil? or i.empty?
      load(file_dna_string_saved?) # Handle default input given.
    else # else batch-process the Array next:
      i.each {|entry| load(entry) }
    end
  else
    i = i.to_s
    # ===================================================================== #
    # Check for i being a number:
    # ===================================================================== #
    if i =~ /^\d+$/i
      entries = Dir['*']
      sorted_entries = entries.sort_by {|entry|
        File.basename(entry).downcase
      }
      i = sorted_entries[i.to_i - 1]
      erev "Using the file #{sfile(i)}.#{rev}"
    end
    if i
      if File.exist? i
        data = File.read(i).chomp
        assign_sequence data
      else
        erev 'Can not read from file '+sfile(i)+rev+
             ' as it does not exist.'
      end
    else
      load_my_file
    end
  end
end

#load_dna ⇒ Object

#

load_dna

This method will assign from the default file.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10790

def load_dna
  _ = file_dna_string_saved?
  if File.exist? _
    erev "Now loading from the file #{sfile(_)}#{rev}."
    assign(_)
  end
end

#load_gtk ⇒ Object

#

load_gtk

Load my gtk module.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8466

def load_gtk
  begin
    require 'gtk_paradise/require_gtk3.rb'
  rescue LoadError; end
end

#load_gtk3_component_aminoacid_composition ⇒ Object

#

load_gtk3_component_aminoacid_composition

#


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# File 'lib/bioroebe/shell/shell.rb', line 8456

def load_gtk3_component_aminoacid_composition
  require 'bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb'
  Bioroebe::GUI::Gtk::AminoacidComposition.run(aminoacid_sequence?)
end

#load_my_file ⇒ Object

#

load_my_file (load tag)

We will use this method to load the shell-file.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4165

def load_my_file
  assign(save_file?, :do_not_upcase)
end

#log_user_input? ⇒ Boolean

#

log_user_input?

Delegate to the class method here, via this wrapper-method.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 1232

def log_user_input?
  ::Bioroebe::Configuration.log_user_input?
end

#main_colour ⇒ Object Also known as: main_col

#

main_colour

#


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# File 'lib/bioroebe/shell/shell.rb', line 8309

def main_colour
  ::Bioroebe.main_colour
end

#mass_weight(i = aminoacids?, , be_verbose = true) ⇒ Object

#

mass_weight (mass_weight tag)

This will calculate the weight of some Aminoacids.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3204

def mass_weight(
    i          = aminoacids?,
    be_verbose = true
  )
  if i.nil? and aminoacids?
    i = aminoacids?
  end
  if i.nil?
    erev 'Please first assign some aminoacids, like GGG.'
  else
    erev 'Now calculating the weight of `'+sfancy(i)+rev+'`.'
    e
    sum = 0
    i.split(//).each {|aminoacid|
      if aminoacid
        weight = ::Bioroebe::AMINO_ACIDS_MASS_TABLE[aminoacid]
        if be_verbose
          erev '  The weight for '+royalblue(aminoacid)+
               rev+
               ' is: '+
                sfancy(
                  weight.to_s.ljust(6,'0').rjust(10)
                )+rev
        end
        sum += weight
      end
    }
    rounded_sum  = sum.round
    n_aminoacids = i.to_s.chars.size 
    erev '  The total sum of these '+simp(n_aminoacids)+rev+
         ' aminoacids (the raw weight) is: '+sfancy(rounded_sum.to_s)
    adjusted_value = sum - ((n_aminoacids - 1) * 18) # 18 for the H2O molecule.
    erev '  The adjusted value (including loss of water '\
         'molecules in the peptide bonds) is: '+
         sfancy(adjusted_value.round(1).to_s)
    e
  end
end

#may_we_show_the_startup_information? ⇒ Boolean

#

may_we_show_the_startup_information?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6280

def may_we_show_the_startup_information?
  @internal_hash[:may_we_show_the_startup_information]
end

#menu(i = command_to_be_passed_to_the_menu?, , report_if_we_did_not_find_the_command = true) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/shell/menu.rb', line 16

def menu(
    i                                     = command_to_be_passed_to_the_menu?,
    report_if_we_did_not_find_the_command = true
  )
  # ======================================================================= #
  # === Handle special instructions given to the second arguments
  # ======================================================================= #
  case report_if_we_did_not_find_the_command
  # ======================================================================= #
  # === :dont_report
  # ======================================================================= #
  when :dont_report,
       :be_quiet,
       :be_quiet_if_the_input_was_not_found
    report_if_we_did_not_find_the_command = false
  end
  if i.is_a?(Array) and !i.empty?
    i.flatten.each {|entry|
      menu(entry, report_if_we_did_not_find_the_command)
    }
  else
    i = i.to_s.strip
    case i # (case tag, casetag, realcase tag)
    # ===================================================================== #
    # === bioroebe --sinatra
    #
    # This entry point starts the sinatra web-interface.
    # ===================================================================== #
    when /^-?-?sinatra2$/i,
         /^-?-?start(_|-| )?sinatra2$/i,
         /^-?-?sinatra$/i
      do_start_the_sinatra_interface
    # ===================================================================== #
    # === mkdir
    # ===================================================================== #
    when /^mkdir$/
      mkdir(f?)
    # ===================================================================== #
    # === no_colours
    # ===================================================================== #
    when 'nocol',
         'noco',
         /^-?-?no(_|-| )?colou?rs?$/,
         /^-?-?disable(_|-| )?colours$/,
         'dcolours'
      disable_colours
    # ===================================================================== #
    # === disable_colours_in_an_extended_manner
    # ===================================================================== #
    when /disable(_|-| )?colours(_|-| )?in(_|-| )?an(_|-| )?extended(_|-| )?manner$/
      disable_colours_in_an_extended_manner(:be_verbose)
    # ===================================================================== #
    # === uniprot
    #
    # This entry point allows the user to download data from uniprot
    # quickly, via the bioshell interface.
    #
    # Invocation examples:
    #
    #   uniprot 2BTS
    #   uniprot A2Z669
    #
    # ===================================================================== #
    when /^uniprot(_|-| )?fetch$/,
         /^uniprot$/i,
         /^unifetch$/i,
         /^fetch(_|-| )?data(_|-| )?from(_|-| )?uniprot$/
      result = uniprot_fetch(f)
      set_result(result)
    # ===================================================================== #
    # === dna_seq?
    # ===================================================================== #
    when 'dna_seq?',
         'dnaseq?',
         'seq?',
         'seqß',
         'dna?',
         'sequence?',
         'string?',
         'sq?',
         'data?',
         's?',
         'show2',
         'show?',
         'report?',
         'print',
         'output',
         /^show(_|-| )?string$/i,
         /^print(_|-| )?dna$/i,
         /^show(_|-| )?dna$/i,
         /^main(_|-| )?string$/i,
         /^show(_|-| )?dna(_|-| )?sequence$/i,
         /^showsequence$/i,
         /^showseq$/i,
         /^dna(_|-| )?string\??$/i,
         'mainstring?',
         'mstring?',
         'dnaß',
         'sdna',
         'normal',
         'DNA?'
      show_dna_sequence
    # ===================================================================== #
    # === Bioroebe.sequence
    # ===================================================================== #
    when 'Bioroebe.sequence?',
         'Bioroebe.seq?'
      e Bioroebe.sequence?
    # ===================================================================== #
    # === dna_sequence?
    # ===================================================================== #
    when /^dna_?sequence\?$/
      pp dna_sequence?
    # ===================================================================== #
    # === fasta?
    # ===================================================================== #
    when 'fasta?',
         /handle_?fasta/ # Feedback information from a local fasta file.
      handle_fasta(a?)
    # ===================================================================== #
    # === chop_to
    #
    # Usage example:
    #
    #   chop_to :ATG
    #
    # ===================================================================== #
    when /^chop_?to$/
      chop_to(a?)
    # ===================================================================== #
    # === chop
    # ===================================================================== #
    when 'chop'
      chop(a?)
    # ===================================================================== #
    # === choppity
    # ===================================================================== #
    when 'choppity',/chop_?codon/
      chop(3)
    # ===================================================================== #
    # === chop33
    # ===================================================================== #
    when /chop(\d+)/ # See: http://rubular.com/r/VWiUYgr5Xq
      chop($1.to_s)
    # ===================================================================== #
    # === default_colours_for_the_aminoacids
    # ===================================================================== #
    when /default(_|-| )?colours(_|-| )?for(_|-| )?the(_|-| )?aminoacids/
      e
      config?.default_colours_for_the_aminoacids.each_pair {|one_letter, colour_to_use|
        e '  '+one_letter+' '+
          ::Colours.send(colour_to_use.to_sym, colour_to_use)+
          rev
      }
      e
    # ===================================================================== #
    # === bioshell_log_dir?
    # ===================================================================== #
    when /bioshell(_|-| )?log(_|-| )?dir\??/i
      e
      e steelblue("  #{log_dir?}bioshell/")
      e
    # ===================================================================== #
    # === dna_to_aminoacids
    #
    # Usage example:
    #
    #   toAA ACGTACGTAGTCATCAGTCAGTA
    #
    # ===================================================================== #
    when /^dna_?to_?aminoacids$/,
         'translate_dna_into_aminoacid',
         'translatednaintoaminoacid',
         'trans',
         'transl',
         'trnas',
         'translateaminoacidintodna',
         'toprotein',
         'to_protein',
         'to_aminoacid',
         'to_aminoacids',
         'aa',
         'toproteins',
         'toaminoacids',
         /to(_|-| )?aa/i,
         'translate',
         'mega',
         'toprotei',
         'translate_aminoacids',
         'toprot',
         'toamin',
         'toamino'
      arguments = a?
      if arguments and arguments.is_a?(Array) and arguments.empty?
        arguments = dna_sequence_as_string?
      end
      show_all_deducible_aminoacid_sequences(arguments)
      if dna_seq?.empty? # This here is ok because the above method checks whether there was a DNA sequence assigned.
        return
      else
        e
        show_protein_composition(
          translate_dna_into_aminoacid(arguments)
        )
        if arguments.empty?
          arguments = dna_sequence?.dup unless a
        end
        ::Bioroebe::DnaToAminoacidSequence.new(arguments)
      end
    # ===================================================================== #
    # === set_dna_sequence
    #
    # Usage examples:
    #
    #   set_sequence /Depot/j/foobar.fasta
    #   set_sequence ACGTACGTACA
    #   set_sequence 555
    #
    # ===================================================================== #
    when 'set_dna_sequence',
         'setdnasequence',
         'setdna',
         'assign',
         'set_dna',
         'assign_sequence',
         'sequence',
         'seq',
         's',
         'asign',
         'set_seq',
         'setseq',
         'assing',
         'set',
         'assig',
         'set_string',
         'setstring',
         'ass',
         'setseq1',
         'setda',
         'read',
         /^assign(_|-| )?dna$/,
         /^assign(_|-| )?this(_|-| )?dna(_|-| )?sequence$/,
         /^set(_|-| )?sequence$/
      set_dna_sequence(a?, :be_verbose) # Always be verbose.
      show_sequence
    # ===================================================================== #
    # === to_mRNA
    # ===================================================================== #
    when /^to(_|-| )?mRNA$/i,
         'mrna',
         /convert_five_prime_dna_into_five_prime_mrna/i
      convert_five_prime_dna_into_five_prime_mrna
    # ===================================================================== #
    # === random
    # ===================================================================== #
    when 'random',
         'rand',
         'ran',
         'ra',
         'random?',
         'rand?',
         'generate',
         'randomseq',
         'ramdpm',
         'setrandom',
         'andom',
         'rando',
         'raond',
         'rnadom',
         'ranom',
         'ranomd',
         'create'
      random(f, remaining_arguments?) # Generate some DNA sequence.
      show_dna_sequence
    # ===================================================================== #
    # === random_dna
    # ===================================================================== #
    when 'random_dna',
         'generate_dna3','generate_dna_variable_composition',
         'generate_random_dna_sequence_with_variable_length_and_variable_composition',
         'generatedna3',
         'generatednavariablecomposition',
         'gdna3',
         'randomdna'
      result = generate_random_dna_sequence_with_variable_length_and_variable_composition
      e result # Display it.
      assign_sequence(result) # And assign it too.
    # ===================================================================== #
    # === is_a_aminoacid?
    #
    # To test this entry point, try:
    #
    #   is_a_aminoacid? Alanin  # => false
    #   is_a_aminoacid? Alanine # => true
    #
    # ===================================================================== #
    when 'is_a_aminoacid?','isaa?'
      pp ::Bioroebe.is_aminoacid?(f?)
    # ===================================================================== #
    # === piped
    # ===================================================================== #
    when 'piped',
         /^show_?codon_?piped_?sequence$/i,
         /^vertical(_|-| )?bar$/i,
         'as_pipe',
         /^codon(_|-| )?piped$/i
      show_codon_piped_sequence
    # ===================================================================== #
    # === pubmed_search
    #
    # Invocation example:
    #
    #   pubmed_search science[journal]+AND+breast+cancer+AND+2008[pdat]
    #
    # ===================================================================== #
    when /^pubmed(_|-| )?search/
      perform_a_pubmed_search(all_arguments?)
    # ===================================================================== #
    # === nohyphen
    #
    # This entry point removes all hyphens.
    #
    # Example:
    #
    #   nohyphen GCA-GCA-AGA-GGA-CTA-AAA-AAA-AAA-CTA-AAA-CTA-ATG-ATG-GCA-GCA-GCA-GCA-GCA
    #
    # ===================================================================== #
    when /nohyphen/
      erev a.join.delete('-')
    # ===================================================================== #
    # === random_aa
    # ===================================================================== #
    when 'random_aa',
         'randomaa',
         'set_random_aminoacids',
         'randomAA',
         'random_aminacids',
         'create_random_aminoacids',
         'random_aminoacids',
         'randomaminoacids'
      set_random_aminoacids
    # ===================================================================== #
    # === all_aminoacids?
    # ===================================================================== #
    when 'all_aminoacids?','display_all_aminoacids','displayallaminoacids',
         'shortnames?',
         'print_aa',
         'printaa',
         'daminoacids',
         'aminoacids_shortnames'
      display_all_aminoacids
    # ===================================================================== #
    # === report_n_start_codons
    #
    # This entry point will report how many start codons can be found
    # in the main Sequence.
    #
    # Invocation example:
    #
    #   report_n_start_codons
    #
    # ===================================================================== #
    when /^report(_|-| )?n(_|-| )?start(_|-| )?codons$/i
      report_n_start_codons
    # ===================================================================== #
    # === palindromes?
    # ===================================================================== #
    when 'palindromes?',
         'PalindromeFinder',
         'pali',
         'palindrome?',
         'pfinder',
         'palindromes'
      ::Bioroebe::PalindromeFinder.new(dna_string?)
    # ===================================================================== #
    # === is_palindrome?
    #
    # Usage examples:
    #
    #   is_palindrome? ATTA
    #   is_palindrome? ATAT
    #
    # ===================================================================== #
    when 'is_palindrome?',
         'ispalindrome?',
         'is_palindrome',
         'is_palindromic?',
         'is_pal?',
         'palindromic?',
         'palinomer?'
      is_palindrome?(f)
    # ===================================================================== #
    # === append
    # ===================================================================== #
    when 'append','<<','merge'
      append(a?) # Call it directly.
    # ===================================================================== #
    # === clear
    # ===================================================================== #
    when 'clear'
      clear(a?)
    # ===================================================================== #
    # === print_aa_table
    # ===================================================================== #
    when 'table_aa','tableaa','print_aa_table','printaatable',
         'molmassen','supertable','table?','maintable',
         'amino_acid_weight','aatable',
         'print_aminoacid_table',
         'patable',
         /^Aminoacids(_|-| )?Mass(_|-| )?Table$/i,
         /^aminoacids(_|-| )?weights\??$/i,
         /^aas(_|-| )?weights\??$/i
      print_aa_table
    # ===================================================================== #
    # === degenerate_primer
    #
    # Invocation example:
    #
    #   dprimer M-T-T-Y-Y-T-A-A-A-STOP
    #
    # ===================================================================== #
    when /^degenerate(_|-| )?primer$/i,
         'degenerate',
         'dprimer', # dprimer M-T-T-Y-Y-T-A-A-A-STOP
         'dprime',
         'dprim',/back_?to_?dna/
      a = aminoacid_sequence? if a.nil? or a.empty?
      dna_sequence = ConvertAminoacidToDNA.new(a?).dna_sequence?.delete('-') # bl $BIOROEBE/convert_aminoacid_to_dna.rb
      erev swarn('Note')+rev+': If you want to assign this DNA sequence to become the new'
      erev 'main sequence, then input:'
      e
      erev orange('  assign_this_dna_sequence')
      e
      @internal_hash[:misc_sequence] = dna_sequence 
    # ===================================================================== #
    # === show_codon_table
    #
    # This entry point can be used to show the (default) codon table,
    # aka the eukaryotic codon table.
    #
    # Usage examples:
    #
    #   ctable
    #   ctable 4
    #
    # ===================================================================== #
    when /^show(_|-)?codon(_|-)?table$/i,
         'codontable?',
         'codontable',
         'codontable2',
         'codon_table?',
         'ctable',
         'ctble',
         'table2',
         'ctable?',
         'alltables'
      show_codon_table(a?)
    # ===================================================================== #
    # === aa_to_dna
    #
    # Translate the aminoacids to the DNA sequence.
    #
    # Usage examples:
    #
    #   aa_to_dna MTTT
    #   aa_to_dna KLMRST
    #
    # ===================================================================== #
    when /^aa(-|_)?to(-|_)?dna$/i
      aa_to_dna(a?)
    # ===================================================================== #
    # === pubmed?
    # ===================================================================== #
    when 'pub',
         'pubmed',
         'pubmed?' # pubmed tag
      pubmed(f?)
    # ===================================================================== #
    # === open_my_files
    # ===================================================================== #
    when /^open(_|-)?my(_|-)?files$/i,
         /^my(_|-)?files$/i,
         'ofiles'
      open_my_files
    # ===================================================================== #
    # === set_codon_table
    # ===================================================================== #
    when 'set_codon_table',
         'setcodontable',
         'codon_table=',
         'ctable=',
         /^choose(_|-)?codon(_|-)?table$/i,
         'choosecodontable',
         'pick_codon_table',
         'codon_table',
         'setcodon',
         'set_codon'
      set_codon_table(f)
    # ===================================================================== #
    # === left_add
    #
    # This will add n nucleotides to the "left" end, aka the 5' end of
    # a DNA or RNA sequence.
    #
    # Invocation example:
    #
    #   left_add 10
    #   ladd 20
    #
    # ===================================================================== #
    when /left(_|-)?add/,
         'ladd'
      left_add(a?)
    # ===================================================================== #
    # === last_input?
    # ===================================================================== #
    when 'last_input?','input?','show_last_input','sli',
         'showlastinput'
      show_last_input
    # ===================================================================== #
    # === human_chromosome_22
    #
    # The human chromosome number 22.
    # ===================================================================== #
    when 'human_chromosome_22'
      _ = 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/chr22.fa.gz'
      e _
      download _
    # ===================================================================== #
    # === sendai
    #
    # The Sendai virus genome, a 15384 bp genome.
    # ===================================================================== #
    when 'sendai'
      e 'https://www.ncbi.nlm.nih.gov/nuccore/9627219'
    # ===================================================================== #
    # === set_start_codon
    # ===================================================================== #
    when 'set_start_codon',
         'setstartcodon',
         'start_codon=',
         'setinitcodon'
      set_start_codon(f)
    # ===================================================================== #
    # === ncbi_taxonomy?
    # ===================================================================== #
    when 'ncbi_taxonomy?'
      browse_to 'http://www.ncbi.nlm.nih.gov/taxonomy/'
    # ===================================================================== #
    # === itax
    # ===================================================================== #
    when 'itax','taxonomy',
         'tax'
      ::Bioroebe::Taxonomy.interactive :run_connected
    # ===================================================================== #
    # === show_remote_urls
    # ===================================================================== #
    when /^show(_|-)?remote(_|-)?urls$/i,
         'url',
         'taxonomy_urls?',
         'remote_url',
         'ncbi?',
         'sremote'
      Bioroebe.show_remote_urls_to_the_NCBI_taxonomy_webpage(f)
    # ===================================================================== #
    # === n_species?
    # ===================================================================== #
    when 'n_species?',
         'n_species',
         'nspecies?',
         'nspecies',
         /^report(_|-| )?n(_|-| )?species$/i
      ::Bioroebe::Taxonomy.report_n_species
    # ===================================================================== #
    # === home?
    # ===================================================================== #
    when /^home\??$/i
      report_where_the_home_directory_can_be_found
    # ===================================================================== #
    # === codon
    #
    # This entry point will quickly show the codon (the aminoacid
    # sequence) of the given input sequence.
    #
    # Usage example:
    #
    #   codon AAAGUCCAUAAA
    #
    # ===================================================================== #
    when 'codon'
      codon(a?)
    # ===================================================================== #
    # === to_rna
    # ===================================================================== #
    when '@rna',
         'to_rna',
         /^-?-?to_?RNA$/i,
         'rna',
         'dna2rna', # You can also use this like so: ATCGTTGC.to_rna
         'rna_translate',
         'rnatranslate',
         'rna?',
         'transcribe',
         'rawrna'
      show_rna_sequence(f)
    # ===================================================================== #
    # === automatically_rename_this_fasta_file
    #
    # This entry-point can be used to automatically rename a FASTA file.
    # ===================================================================== #
    when /^-?-?automatically(_|-)?rename(_|-)?this(_|-)?fasta(_|-)?file$/i,
         /^-?-?infer(_|-)?fasta$/i,
         /^-?-?ifasta$/i
      automatically_rename_this_fasta_file(a)
    # ===================================================================== #
    # === show_both_strands
    # ===================================================================== #
    when 'show_both_strands',
         'both','dual',
         'showbothstrands',
         /^-?-?show(_|-)?both(_|-)?dna(_|-)?strands$/i,
         'double',
         'show_double_strand',
         /^dsDNA$/i
      show_both_dna_strands
    # ===================================================================== #
    # === UAG?
    # ===================================================================== #
    when /^UAG\??$/i
      this_sequence = dna_string?
      use_this_start_codon = 'UAG'
      if this_sequence.include? 'U'
      else
        use_this_start_codon = 'TAG'
      end
      _ = search_sequence_for_open_reading_frames(
        this_sequence,
        :frame1, # use_which_frame
        use_this_start_codon
      )
      if _.empty?
        erev 'No substring '+i.to_s.delete('?')+' was found.'
      else
        show_nucleotide_sequence?.display(i) {{ colourize_this_subsequence: use_this_start_codon }}
      end
    # ===================================================================== #
    # === size?
    # ===================================================================== #
    when 'size?',
         'nuc?',
         'size',
         'nsizes',
         'nsize',
         'length?',
         'len?',
         'len',
         'report_length_of_the_dna_string',
         'sizeß',
         'n?'
      report_size_of(f?)
    # ===================================================================== #
    # === find_orfs
    # ===================================================================== #
    when 'find_orfs',
         /^find(_|-)?all(_|-)?orfs$/i,
         'forfs','forf'
      find_all_orfs
    # ===================================================================== #
    # === prepend_start
    # ===================================================================== #
    when 'pstart',
         'prepend_start',
         'appendstart',
         'start'
      add_to_start :start
    # ===================================================================== #
    # === fancy
    # ===================================================================== #
    when 'fancy'
      display_open_reading_frames
    # ===================================================================== #
    # === fetch
    #
    # This entry point allows the user to fetch a (remote) .pdb file.
    #
    # Invocation example:
    #
    #   fetch 2BTS
    #
    # ===================================================================== #
    when /^fetch(_|-)?from(_|-)?pdb$/,
         'fetch'
      fetch_from_pdb(f)
    # ===================================================================== #
    # === reverse_complement
    #
    # This entry point will build the "reverse complement" sequence
    # to a given DNA sequence at hand.
    # ===================================================================== #
    when /^reverse(_|-)?complement$/i,
         /^rev(_|-)?complement$/i,
         'rcomplement',
         'rcompl'
      reverse_complement(f)
    # ===================================================================== #
    # === P00995
    # ===================================================================== #
    when 'P00995'
      oib 'https://www.uniprot.org/uniprot/P00995'
      download_this_fasta_sequence 'https://www.uniprot.org/uniprot/P00995.fasta'
    # ===================================================================== #
    # === brenda
    # ===================================================================== #
    when /^brenda$/i
      open_in_browser('https://www.brenda-enzymes.org/')
    # ===================================================================== #
    # === expasy
    # ===================================================================== #
    when /^expasy$/i
      open_expasy(a?)
    # ===================================================================== #
    # === 9cutters
    # ===================================================================== #
    when '9cutter',
         '9cutters',
         '9-cutters',
         '9cut'
      show_restriction_enzymes '9'
    # ===================================================================== #
    # === code?
    # ===================================================================== #
    when 'code?','code','translate_aminoacids_into_dna'
      translate_aminoacids_into_dna(a?)
    # ===================================================================== #
    # === wormbase?
    # ===================================================================== #
    when 'wormbase?',
         'wormbase'
      e (_ = Bioroebe.try_to_pass_through_beautiful_url(_))
        open_in_browser _
    # ===================================================================== #
    # === promoters?
    # ===================================================================== #
    when /^promoters?\??$/,
         /^search_?for_?known_?promoters$/
      search_for_known_promoters
    # ===================================================================== #
    # === samino
    # ===================================================================== #
    when 't2','translate2','aminoacid??','shorten',
         /shorten_?aminoacid/,'samino',
         'saminoacid'
      shorten_aminoacid(a?)
    # ===================================================================== #
    # === frameshift
    # ===================================================================== #
    when 'frameshift','frame','shift','shifter','shifting',
         'perform_frameshift_action','performframeshiftaction',
         'fr','frame?'
      perform_frameshift_action(a?)
    # ===================================================================== #
    # === GPCR?
    # ===================================================================== #
    when 'GPCR?','gpcr?'
      _ = 'http://www.gpcr.org/7tm/'
      e simp(_)+rev
      set_xorg_buffer(_) if @configuration.additionally_set_xorg_buffer
    # ===================================================================== #
    # === generate_random_protein_sequence_with_variable_length_and_variable_composition'
    # ===================================================================== #
    when /^generate(_|-)?random(_|-)?protein(_|-)?sequence(_|-)?with(_|-)?variable(_|-)?length(_|-)?and(_|-)?variable(_|-)?composition$/
      generate_random_protein_sequence_with_variable_length_and_variable_composition
    # ===================================================================== #
    # === wobble?
    # ===================================================================== #
    when 'wobble',
         'wobble?'
      erev 'CAGUI, G->C(U) und U->A(G)sowie I->U,C,A, an der '\
           '5 Prime Position der tRNA.'
    # ===================================================================== #
    # === RNAfold2
    # ===================================================================== #
    when 'RNAfold2'
      esystem 'RNAfold -p --MEA < test.seq'
    # ===================================================================== #
    # === nucleotide_position?
    # ===================================================================== #
    when 'nucleotide_position?',
         'nucleotideposition?',
         'position?'
      show_position_for_the_main_sequence
    # ===================================================================== #
    # === find_gene
    # ===================================================================== #
    when 'find_gene',
         'findgene',
         'fgene',
         'genes?',
         'fingene'
      find_gene(a?)
    # ===================================================================== #
    # === to_talen
    # ===================================================================== #
    when /^to(-|_| )?talen$/,
         'talen',
         '2talen'
      to_talen(a?)
    # ===================================================================== #
    # === debug
    # ===================================================================== #
    when 'debug',
         'deb'
      f 'Toggling debug from '+sfancy(debug?.to_s)+' to: '
      do_toggle_debug_value
      e debug?
    # ===================================================================== #
    # === 2cutters
    # ===================================================================== #
    when '2cutter',
         '2cutters',
         '2-cutters',
         '2cut'
      show_restriction_enzymes '2'
    # ===================================================================== #
    # === 3cutters
    # ===================================================================== #
    when '3cutter',
         '3cutters',
         '3-cutters',
         '3cut'
      show_restriction_enzymes '3'
    # ===================================================================== #
    # === Handle input such as "658-660 =     CCA"
    # ===================================================================== #
    when /^(\d+)(\.\.|-)(\d+)\s*=\s*(.*)$/ # See: https://rubular.com/r/hDLHLND7cc
      _ = dna_sequence? # Keep a reference copy.
      start_position = $1.to_s.to_i # 11-12 = AA
      end_position   = $3.to_s.to_i
      new_sequence   = $4.to_s.strip
      old_sequence   = _[start_position-1, (end_position - start_position)+1]
      erev 'We will perform a match assignment at nucleotide position '+
           start_position.to_s+'-'+end_position.to_s+rev+
           '. The'
      erev 'old subsequence was: '+sfancy(old_sequence)+rev+
           ' - the new subsequence will be '+simp(new_sequence)
      new_sequence.delete!("'")
      _[start_position-1, (end_position - start_position)+1] = new_sequence
      set_dna_sequence(_)
    # ===================================================================== #
    # === dna_analyze
    # ===================================================================== #
    when /^dna(_|-)?analyze$/,
         'danalyze'
      analyze(a?) { :dna }
    # ===================================================================== #
    # === dash
    # ===================================================================== #
    when 'dash',
         'dashed',
         'spacer',
         /^splitted(_|-)?form$/
      show_sequence_in_splitted_form(f,'-')
    # ===================================================================== #
    # === leucine_zippers?
    # ===================================================================== #
    when 'leucine_zippers?','scan_for_leucine_zippers','leucine?',
         'leucinez','zippers','l?','leu?'
      scan_for_leucine_zippers(a?)
    # ===================================================================== #
    # === @aminoacids
    # ===================================================================== #
    when '@aminoacids'
      pp @internal_hash[:aminoacids]
    # ===================================================================== #
    # === open
    # ===================================================================== #
    when /^open$/i
      if f
        open(f)
      else
        open_my_files
      end
    # ===================================================================== #
    # === size_rna
    # ===================================================================== #
    when /^size(_|-)?rna$/i
      e @internal_hash[:rna].sequence.size.to_s
    # ===================================================================== #
    # === toggle_truncate
    # ===================================================================== #
    when /^toggle(_|-)?truncate$/i,
         /^truncate$/i
      toggle_truncate
    # ===================================================================== #
    # === 9mer
    # ===================================================================== #
    when '9mer',
         '9mer?'
      erev 'TTA|TCC|ACA'
      find_in_main_sequence('TTATCCACA')
      erev 'We found the 9mer n times: '+
            sfancy(string?.scan('TTATCCACA').size.to_s)
    # ===================================================================== #
    # === TAG?
    # ===================================================================== #
    when /^TAG\??$/i
      _ = search_sequence_for_open_reading_frames(
        i                    = string?,
        use_which_frame      = :frame1,
        use_this_start_codon = 'TAG'
      )
      if _.empty?
        erev 'No substring '+i.to_s.delete('?')+' was found.'
      else
        show_nucleotide_sequence?.display(i) {{ colourize_this_subsequence: use_this_start_codon }}
      end
    # ===================================================================== #
    # === inicodon?
    # ===================================================================== #
    when 'inicodon?',
         'startcodon?'
      erev ::Bioroebe.start_codon?
    # ===================================================================== #
    # === default_stop_codons?
    # ===================================================================== #
    when 'default_stop_codons?',
         'dstop?',
         'dna_codons?',
         'dna_codons',
         'dnacodons'
      pp ::Bioroebe.stop_codons? # This will be an Array.
    # ===================================================================== #
    # === discover_all_palindromes
    # ===================================================================== #
    when /^discover(_|-)?all(_|-)?palindromes$/i,
         /^dpalindromes$/i,
         'dpal'
      discover_all_palindromes(f)
    # ===================================================================== #
    # === dotplot
    # ===================================================================== #
    when /^dotplot$/i
      show_2D_dotplot(a?)
    # ===================================================================== #
    # === set_length
    # ===================================================================== #
    when /^set(_|-)?length$/i,
         /^set_?maxlength/,
         'length',
         'maxlength',
         'maxlen'
      set_default_length(a, :be_verbose)
    # ===================================================================== #
    # === replay
    # ===================================================================== #
    when 'replay',
         /^save(_|-)?history$/i
      replay(f)
    # ===================================================================== #
    # === raw_aa
    #
    # This entry point will simply display the raw aminoacid sequence,
    # translated from the main DNA sequence.
    # ===================================================================== #
    when /^raw(_|-)?aa$/i
      i = dna_sequence?
      sequence = ::Bioroebe::DnaToAminoacidSequence.new(i) { :be_quiet }.sequence
      e sequence
    # ===================================================================== #
    # === RNAfold3
    # ===================================================================== #
    when 'RNAfold3'
      esystem 'RNAfold -p < 5S.seq'
      esystem 'mountain.pl 5S_dp.ps | xmgrace -pipe'
      esystem 'relplot.pl 5S_ss.ps 5S_dp.ps > 5S_rss.ps'
    # ===================================================================== #
    # === mutate_position
    # ===================================================================== #
    when 'mutate_position','mutateposition','mposition','mpos'
      do_mutate_dna_sequence_at_this_nucleotide_position(a?) # mutate_position 5 C
    # ===================================================================== #
    # === include?
    # ===================================================================== #
    when 'include?',
         'inc?'
      include? f
    # ===================================================================== #
    # === cut
    # ===================================================================== #
    when /^cut$/i,
         'cutter'
      cut(f)
    # ===================================================================== #
    # === parse_gff
    # ===================================================================== #
    when /^-?-?parse(_|-)?gff$/i,
         'gff',
         'gff3',
         'gff?',
         'gff3?',
         /^-?-?scan(_|-)?gff$/i
      scan_or_parse_for_this_gff_file_or_any_gff_file(a?)
    # ===================================================================== #
    # === find
    # ===================================================================== #
    when /^try(_|-)?to(_|-)?find(_|-)?restriction(_|-)?enzymes(_|-)?for$/i,
         /scan(_|-)?for$/i,
         /look(_|-)?for$/i,
         'lfor',
         'find',
         'ind',
         'scan'
      try_to_find_restriction_enzymes_for(a?) # look_for
    # ===================================================================== #
    # === header?
    # ===================================================================== #
    when /^header\??$/i,
         /^headers\??$/i,
         /^show(_|-)?header(_|-)?of$/i
      show_header_of(a?)
    # ===================================================================== #
    # === uncolourize_this_aminoacid
    # ===================================================================== #
    when 'uncolourize',
         'uncolourize_this_aminoacid',
         'uncolourizethisaminoacid',
         'uncolaa',
         'uncola',
         '-colaa',
         'colremove',
         'ucola'
      uncolourize_this_aminoacid(f)
    # ===================================================================== #
    # === split
    # ===================================================================== #
    when 'split',
         'show_sequence_in_splitted_form'
      show_sequence_in_splitted_form(f)
    # ===================================================================== #
    # === namespace?
    # ===================================================================== #
    when 'namespace?'
      e namespace?
    # ===================================================================== #
    # === segments?
    # ===================================================================== #
    when 'segments?',
         'show_segments',
         'segments',
         'segmente'
      show_segments
    # ===================================================================== #
    # === to_rna2
    # ===================================================================== #
    when 'to_rna2'
      to_rna(f)
    # ===================================================================== #
    # === pathways?
    # ===================================================================== #
    when 'pathways?',
         'pathways',
         'pways',
         'pathway?',
         'pathway',
         'meta?',
         'path?',
         'show_all_pathways'
      show_all_pathways
    # ===================================================================== #
    # === aa_families?
    # ===================================================================== #
    when 'aa_families?',
         'aafamilies?',
         'aafamilies'
      pp ::Bioroebe.aa_families?
    # ===================================================================== #
    # === pfam?
    # ===================================================================== #
    when 'pfam?','pfam'
      e 'https://pfam.sanger.ac.uk/'
    # ===================================================================== #
    # === add
    # ===================================================================== #
    when 'add'
      add(a?)
    # ===================================================================== #
    # === set_padding
    # ===================================================================== #
    when /set_?padding/,
         'padding'
      set_padding(f, :be_verbose) # setpadding
    # ===================================================================== #
    # === ccaat?
    # ===================================================================== #
    when 'ccaat?',
         /^show(_|-)?ccaat(_|-)?sites$/,
         'ccaat',
         'ccaa'
      show_ccaat_sites
    # ===================================================================== #
    # === analyze
    # ===================================================================== #
    when 'analyze','ana?','analyze?'
      analyze(a?)
    # ===================================================================== #
    # === SSR?
    # ===================================================================== #
    when 'SSR?','ssr?','SSR','single_sequence_repeats'
      e generate_single_sequence_repeats
    # ===================================================================== #
    # === nucleotide?
    # ===================================================================== #
    when 'nucleotide?',
         'nucleotide',
         'ncbi_nucleotide_search_for'
      ncbi_nucleotide_search_for(a?)
    # ===================================================================== #
    # === three_letters_to_one_letter
    #
    # Usage example:
    #
    #   three_letters_to_one_letter THR
    #
    # ===================================================================== #
    when /^three(_|-)?letters(_|-)?to(_|-)?one(_|-)?letter$/i
      e three_letters_to_one_letter(a?)
    # ===================================================================== #
    # === rest_enzymes
    # ===================================================================== #
    when /^rest(_|-)?enzymes$/
      pp ::Bioroebe.show_restriction_enzymes
    # ===================================================================== #
    # === cutseq
    # ===================================================================== #
    when /^cutse(q|t)?$/i
      cutseq(a?)
    # ===================================================================== #
    # === first
    # ===================================================================== #
    when 'first',
         /^change(_|-)?first(_|-)?nucleotide(_|-)?to$/
      first(f)
    # ===================================================================== #
    # === pdf?
    # ===================================================================== #
    when 'pdf?','report_where_the_pdf_tutorial_can_be_found'
      report_where_the_pdf_tutorial_can_be_found
    # ===================================================================== #
    # === dmp?
    # ===================================================================== #
    when 'dmp?',
         /^show(_|-)?all(_|-)?dmp(_|-)?files$/,
         'dmp'
      show_all_dmp_files
    # ===================================================================== #
    # === codon?
    #
    # Invocation example in the BioShell:
    #
    #   codon? ATG
    #
    # ===================================================================== #
    when 'codon?',
         'kazusa_codon'
      show_codons_of_this_aminoacid_or_show_kazusa_codon(a?)
    # ===================================================================== #
    # === do_not_show_the_trailer
    # ===================================================================== #
    when /^-?-?do_?not_?show_?the_?trailer$/,
         /^-?-?no_?trailer$/
      do_not_show_the_trailer
    # ===================================================================== #
    # === edit
    # ===================================================================== #
    when /^edit$/i
      open_this_file_in_editor :bioshell
    # ===================================================================== #
    # === mpsa_source
    # ===================================================================== #
    when /^-?-?mpsa_?source/
      e '/opt/MPSA/mpsa/mpsa.bashrc'
    # ===================================================================== #
    # === assume?
    # ===================================================================== #
    when 'assume?',
         'assume',
         'assume_what_type_this_is'
      assume_what_type_this_is(a?) # assume ATTGGCCCATATTGGCC
    # ===================================================================== #
    # === bparse
    # ===================================================================== #
    when 'bparse',
         /^biolang(_|-)?parser$/
      BiolangParser.new # bl $BIOROEBE/biolang_parser.rb
    # ===================================================================== #
    # === set_prompt
    # ===================================================================== #
    when /^set(_|-)?prompt$/,
         'prompt',
         'setpwd'
      set_prompt(f)
    # ===================================================================== #
    # === no_prompt
    # ===================================================================== #
    when /^no(_|-)?prompt$/i
      set_prompt :empty
    # ===================================================================== #
    # === pyranose 2-oxidase
    # ===================================================================== #
    when /^pyranose(-|_)?2(-|_)?oxidase$/i
      e
      erev 'https://www.ncbi.nlm.nih.gov/nuccore/XM_008046051.1'
      e
    # ===================================================================== #
    # === disulfide?
    #
    # This entry point can be used to show disulfide positions in the
    # given sequence.
    # ===================================================================== #
    when /^-?-?disulfide\??$/i,
         /^-?-?show(_|-)?disulfides$/i
      show_disulfides
    # ===================================================================== #
    # === colourize_this_aminoacid
    # ===================================================================== #
    when 'colourize',
         /^colourize(_|-)?this(_|-)?aminoacid$/,
         'colaa',
         'cola',
         'colAA',
         'colourize_aminoacid'
      colourize_this_aminoacid(f)
    # ===================================================================== #
    # === frame2
    # ===================================================================== #
    when 'frame2',
         'f2'
      showorf(dna_sequence?, :frame2)
    # ===================================================================== #
    # === frame3
    # ===================================================================== #
    when 'frame3',
         'f3'
      showorf(dna_sequence?, :frame3)
    # ===================================================================== #
    # === mutate_aminoacid_position
    # ===================================================================== #
    when /^mutate(_|-)?aminoacid(_|-)?position$/
      mutate_aminoacid_position(a?)
    # ===================================================================== #
    # === interactive_colour_menu
    # ===================================================================== #
    when /^interactive(_|-)?colour(_|-)?menu$/,
         'icolours'
      interactive_colour_menu
    # ===================================================================== #
    # === aligned
    # ===================================================================== #
    when 'aligned',
         'aligned?',
         'beauty',
         'beautified', # We show the DNA sequence correctly aligned.
         'formatted',
         'padded',
         'beaut',
         'falign',
         'blocked',
         'block',
         /^show(_|-)?this(_|-)?sequence(_|-)?padded$/i
      show_this_sequence_padded(a?)
    # ===================================================================== #
    # === all_arguments
    # ===================================================================== #
    when /^arguments\??$/i
      pp all_arguments?
    # ===================================================================== #
    # === do
    #
    # do_action() as name is better than do(), in my opinion.
    # ===================================================================== #
    when 'do',
         /^do(_|-)?action$/i
      do_action(a?)
    # ===================================================================== #
    # === glutathione
    # ===================================================================== #
    when 'glutathione','glutathion'
      set_aminoacids('GCG')
    # ===================================================================== #
    # === relion_tags
    # ===================================================================== #
    when /^relion(_|-)?tags$/,
         'relion_tags?'
      e
      erev '_rlnImageName' 
      erev '_rlnCoordinateX' 
      erev '_rlnCoordinateY' 
      erev '_rlnMicrographName'
      erev '_rlnImageName'
      erev '_rlnDefocusU'
      erev '_rlnDefocusV'
      erev '_rlnDefocusAngle'
      erev '_rlnVoltage'
      erev '_rlnAmplitudeContrast'
      erev '_rlnSphericalAberration'
      e
    # ===================================================================== #
    # === project_base_dir
    # ===================================================================== #
    when /^project(_|-)?base(_|-)?dir$/i,
         'pdir',
         /^PROJECT(_|-)?BASE(_|-)?DIRECTORY$/i
      e Bioroebe.project_base_directory?
    # ===================================================================== #
    # === set_search
    # ===================================================================== #
    when /^set(_|-)?search$/i,
         /^set(_|-)?sequence$/i,
         /^set(_|-)?search(_|-)?string$/i,
         /^set(_|-)?search(_|-)?sequence$/i
      set_search_for(a?)
    # ===================================================================== #
    # === balanced
    # ===================================================================== #
    when /^create(_|-)?balanced(_|-)?composition$/i,
         'balanced'
      set_dna_string(
        create_balanced_composition(a?)
      )
    # ===================================================================== #
    # === show_local_sequences
    #
    # This entry point shows all local FASTA sequences - typically via
    # .fa or .fasta files.
    # ===================================================================== #
    when 'local_sequences?',
         'show_local_sequences',
         'showlocalsequences',
         'localfasta',
         'sequences?',
         'local?',
         'fastasequences?',
         'show_fasta_files',
         'localfasta?',
         'lfasta',
         /fasta(_|-)?files\??/
      show_local_sequences
      show_hint_how_to_use_the_local_sequences
    # ===================================================================== #
    # === compact_file
    # ===================================================================== #
    when /^compact(_|-)?file$/i,
         'compact',
         'cfile',
         'compacter'
      compact_file(f)
    # ===================================================================== #
    # === peroxisome_pts2
    # ===================================================================== #
    when 'peroxisome_pts2'
      erev 'H₂N-----Arg-Leu-X5-His-Leu-'
    # ===================================================================== #
    # === dna_translate
    # ===================================================================== #
    when /^dna(_|-)?translate/
      dna_translate(all_arguments?)
    # ===================================================================== #
    # === 1igt.pdb
    # ===================================================================== #
    when '1igt.pdb'
      erev 'https://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=366A3EE'
    # ===================================================================== #
    # === MG1655
    # ===================================================================== #
    when 'MG1655'
      e
      efancy '  https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP032667.1'
      e
    # ===================================================================== #
    # === @configuration
    # ===================================================================== #
    when '@configuration'
      pp @configuration
    # ===================================================================== #
    # === colours?
    # ===================================================================== #
    when 'colours?','ucolours?','ucolours',
         /^will(_|-)?we(_|-)?use(_|-)?colours\??$/i
      will_we_use_colours?
    # ===================================================================== #
    # === @use_working_directory_as_prompt
    # ===================================================================== #
    when '@use_working_directory_as_prompt'
      pp @internal_hash[:use_working_directory_as_prompt]
    # ===================================================================== #
    # === uniprot?
    # ===================================================================== #
    when 'uniprot?',
         /^open(_|-)?in(_|-)?uniprot$/,
         'prot'
      open_in_uniprot(f)
    # ===================================================================== #
    # === HU?
    # ===================================================================== #
    when 'HU?',
         'heat-unstable',
         'heat-unstable-protein'
      erev 'heat-unstable protein in E. coli.'
      erev 'Encoded by hupA and hupB gene - see these links:'
      erev 'hupA:'
      erev '  '+NCBI_GENE+'948499'
      erev '  https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.3?report=fasta&from=4200281&to=4200553'
      erev 'hupB:'
      erev '  '+NCBI_GENE+'949095'
      erev '  https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.3?report=fasta&from=461451&to=461723'
    # ===================================================================== #
    # === snuc
    #
    # Invocation example:
    #
    #   snuc lady slipper orchid
    #
    # ===================================================================== #
    when /^search(_|-)?for(_|-)?nucleotide(_|-)?sequence/i,
         'snuc'
      search_for_nucleotide_sequence(a?) # Delegate into: http://www.ncbi.nlm.nih.gov/nucgss?term=G
    # ===================================================================== #
    # === fasta_header?
    # ===================================================================== #
    when /^show(_|-)?fasta(_|-)?headers$/i,
         'sfasta',
         /^fasta(_|-)?header\??/i,
         'showfasta',
         'fheader'
      show_fasta_headers(f)
    # ===================================================================== #
    # === copyright?
    # ===================================================================== #
    when /^copyright\??$/i
      show_copyright_clause
    # ===================================================================== #
    # === pBR322?
    # ===================================================================== #
    when /pBR322\??/
      e
      erev '  https://www.ncbi.nlm.nih.gov/nuccore/208958?report=fasta' # The pBR322 sequence.
      e
    # ===================================================================== #
    # === ARRAY_WITH_COMPLETIONS
    # ===================================================================== #
    when /^ARRAY(_|-)?WITH(_|-)?COMPLETIONS$/i
      pp ARRAY_WITH_COMPLETIONS
    # ===================================================================== #
    # === @array_these_sequences_were_chopped_away
    #
    # This entry point is mostly used for debugging-purposes.
    # ===================================================================== #
    when '@array_these_sequences_were_chopped_away',
         'chopped?'
      pp @internal_hash[:array_these_sequences_were_chopped_away]
    # ===================================================================== #
    # === array_colourize_this_aminoacid
    # ===================================================================== #
    when 'array_colourize_this_aminoacid'
      pp ::Bioroebe.array_colourize_this_aminoacid
    # ===================================================================== #
    # === @array_sequences
    # ===================================================================== #
    when '@array_sequences'
      pp array_sequences?
    # ===================================================================== #
    # === identical?
    # ===================================================================== #
    when 'identical?',
         'identical',
         'same',
         'same_content?',
         'similar?',
         'compare_two_files',
         'comparetwofiles'
      compare_two_files(f, second_argument)
    # ===================================================================== #
    # === locus?
    # ===================================================================== #
    when 'locus?'
      e @internal_hash[:locus]
    # ===================================================================== #
    # === molmass?
    # ===================================================================== #
    when 'mass?',
         'molecularmass?',
         'molmass?',
         'mmass',
         /^molecular(_|-)?mass(_|-)?of(_|-)?amino(_|-)?acids(_|-)?in(_|-)?the(_|-)?sequence$/i
      molecular_mass_of_amino_acids_in_the_sequence(f)
    # ===================================================================== #
    # === +
    #
    # Show the positively charged aminoacids.
    # ===================================================================== #
    when '+',
         'show_the_positively_charged_aminoacids'
      show_the_positively_charged_aminoacids
    # ===================================================================== #
    # === insulin?
    # ===================================================================== #
    when 'insulin?'
      show_insulin_entries_at_NCBI
    # ===================================================================== #
    # === list
    # ===================================================================== #
    when 'list'
      list(a?)
    # ===================================================================== #
    # === configdir?
    # ===================================================================== #
    when 'configdir?',
         /^show(_|-)?config(_|-)?dir$/i
      show_config_dir
    # ===================================================================== #
    # === show_nucleotides_table
    # ===================================================================== #
    when 'nucleotides?','nucleotide_table','nucleotidetable',
         'nucleotide_table?','nucleotidetable?','stable',
         'show_nucleotides_table','shownucleotidestable',
         'nucleotides_table?'
      show_nucleotides_table
    # ===================================================================== #
    # === print_table
    # ===================================================================== #
    when 'print_table','table','aa?','aminoacid_information',
         'print_aminoacid_information_table','aainfo',
         'aminosäuren','aminoacids','ptable','shortcuts?',
         'ainfo?','aainfo?','printtable','aa_table',
         'aminoacidstable?','aatable?'
      print_aminoacid_information_table
    # ===================================================================== #
    # === assigned?
    # ===================================================================== #
    when /assigned\??/,
         /is(_|-)?any(_|-)?nucleotide(_|-)?assigned\??/
      if is_any_nucleotide_assigned?
        erev 'A nucleotide sequence is assigned.'
      else
        erev 'No nucleotide sequence is assigned.'
      end
    # ===================================================================== #
    # === set_jumper_dir
    # ===================================================================== #
    when /set_?jumper_?dir/,'set_jumper','setjumper','sjumper'
        set_jumper_directory(f)
    # ===================================================================== #
    # === extract_sequence
    # ===================================================================== #
    when /extract_?sequence/,'extract','ext'
      extract_sequence(a?)
    # ===================================================================== #
    # === no_newlines
    # ===================================================================== #
    when /no_?newlines/
      no_newlines(a?)
    # ===================================================================== #
    # === run_sql_query
    # ===================================================================== #
    when 'run_sql_query','runsqlquery' # Input a sql command directly.
      run_sql_query(f)
    # ===================================================================== #
    # === Restriction enzymes
    #
    # Usage example for rest:
    #   rest AAAAAAAAGGCGCCCTGACCATCTAGAAAAA
    # ===================================================================== #
    when 'Bioroebe.restriction_enzymes?','all_restriction_enzymes',
         'allrestrictionenzymes'
      pp ::Bioroebe.restriction_enzymes?
    # ===================================================================== #
    # === search
    # ===================================================================== #
    when 'search','run',/start_?search/
      start_search
    # ===================================================================== #
    # === URLs?
    # ===================================================================== #
    when 'URLs?','URL?','URLS?',/show_?useful_?URLs/
      show_useful_URLs
    # ===================================================================== #
    # === NM_021964.1
    # ===================================================================== #
    when 'NM_021964.1','NM_021964' # This should one day be replaced with a NCBI-query system.
      e 'https://www.ncbi.nlm.nih.gov/nuccore/NM_021964.1'
      e 'https://www.ncbi.nlm.nih.gov/nuccore/NM_021964' # ← This is the updated variant.
    # ===================================================================== #
    # === first_orf?
    # ===================================================================== #
    when /first_?orf\??/,/show_?first_?orf/,'1storf','1st_ORF','1stORF'
      show_first_orf
    # ===================================================================== #
    # === emicroscopy
    # ===================================================================== #
    when 'emicroscopy'
      e 'This has not been ported yet - stay tuned.'
    # ===================================================================== #
    # === 4cutters
    # ===================================================================== #
    when '4cutter','4cutters','4-cutters','4cut'
      show_restriction_enzymes '4'
    # ===================================================================== #
    # === 5cutters
    # ===================================================================== #
    when '5cutter','5cutters','5-cutters','5cut'
      show_restriction_enzymes '5'
    # ===================================================================== #
    # === 6cutters
    # ===================================================================== #
    when '6cutter','6cutters','6-cutters','6cut'
      show_restriction_enzymes '6'
    # ===================================================================== #
    # === 7cutters
    # ===================================================================== #
    when '7cutter','7cutters','7-cutters','7cut'
      show_restriction_enzymes '7'
    # ===================================================================== #
    # === 8cutters
    # ===================================================================== #
    when '8cutter','8cutters','8-cutters','8cut'
      show_restriction_enzymes '8'
    # ===================================================================== #
    # === rawseq
    # ===================================================================== #
    when /rawseq\??/,
         'rawstring',
         'rawstring?',
         /dna_?sequence\??/,
         'fullseq',
         'realseq'
      e string? 
    # ===================================================================== #
    # === mutate
    # ===================================================================== #
    when 'mutate',
         'mutate_dna_sequence',
         'mutatednasequence'
      mutate_dna_sequence(a?)
    # ===================================================================== #
    # === setseq2
    # ===================================================================== #
    when /setseq2/, /seq2[^\?]/
      set_sequence_2(a?)
    # ===================================================================== #
    # === setseq3
    # ===================================================================== #
    when /setseq3/, /seq3[^\?]/
      set_sequence_3(a?)
    # ===================================================================== #
    # === setseq4
    # ===================================================================== #
    when /setseq4/, /seq4[^\?]/
      set_sequence_4(a?)
    # ===================================================================== #
    # === setseq5
    # ===================================================================== #
    when /setseq5/, /seq5[^\?]/
      set_sequence_5(a?)
    # ===================================================================== #
    # === setseq6
    # ===================================================================== #
    when /setseq6/, /seq6[^\?]/
      set_sequence_6(a?)
    # ===================================================================== #
    # === date
    # ===================================================================== #
    when 'date','show_date','showdate','sdate'
      show_date
    # ===================================================================== #
    # === colour_scheme_demo
    # ===================================================================== #
    when 'colour_scheme_demo','colourschemedemo','colour_tests',
         'colourtests','colourdemo'
      colour_scheme_demo
    # ===================================================================== #
    # === colour_scheme_for_aa
    # ===================================================================== #
    when 'colour_scheme_for_aa','colourschemeforaa',
         'colour_scheme_for_aminoacids','colour_scheme2',
         'caa','scheme_aa'
      colour_scheme_for_aminoacids(a?)
    # ===================================================================== #
    # === n_uracil?
    # ===================================================================== #
    when 'n_uracil?',
         'n_uracil',
         'nuracil',
         'nuracil?'
      n_uracil?
    # ===================================================================== #
    # === sixpack
    # ===================================================================== #
    when 'sixpack',
         '6pack',
         'show_sixpack_alignment','showsixpackalignment'
      show_sixpack_alignment(a?)
    # ===================================================================== #
    # === compseq
    #
    # This entry point is a wrapper over "compare sequence" aka compseq.
    # ===================================================================== #
    when 'compseq',
         'compseq?',
         /^compare(_|-)?the(_|-)?sequence$/i,
         'analyze_the_sequence',
         'csequ',
         'cseq',
         'compsqe',
         /^frequency(_|-)?analyzer$/i,
         'emboss',
         /^emboss(_|-)?compseq$/i,
         'dinucleotides',
         /^nucleotide(_|-)?frequency$/i
      compseq(a?) # bl compseq
    # ===================================================================== #
    # === show
    # ===================================================================== #
    when 'show',
         /^do(_|-)?show$/i
      show(a?)
    # ===================================================================== #
    # === generate_palindrome
    # ===================================================================== #
    when /^generate(_|-)?palindrome$/i,
         'palindrome',
         'palindrom',
         'pal',
         'pdrome'
      generate_palindrome(a?)
    # ===================================================================== #
    # === bioroebe --tk1                                           (tk tag)
    # ===================================================================== #
    when /^-?-?tk1$/i
      require 'bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb'
      Bioroebe::GUI::Tk::AminoacidComposition.new(ARGV)
    # ===================================================================== #
    # === bioroebe --tk2
    #
    # Invocation example:
    #
    #   bioroebe --tk-three-to-one
    #
    # ===================================================================== #
    when /^-?-?tk2$/i,
         /^-?-?tk(_|-| )?three(_|-| )?to(_|-| )?one$/i
      tk_start_three_to_one
    # ===================================================================== #
    # === bioroebe --tk3
    #
    # Invocation example:
    #
    #   bioroebe --tk3
    #
    # ===================================================================== #
    when /^-?-?tk3$/i
      require 'bioroebe/gui/tk/hamming_distance/hamming_distance.rb'
      Bioroebe::GUI::Tk::HammingDistance.new(ARGV)
    # ===================================================================== #
    # === start_and_stop?
    # ===================================================================== #
    when /^start_?and_?stop\??/
      report_colourized_sequence(:start_and_stop_codon)
    # ===================================================================== #
    # === start_and_stop
    # ===================================================================== #
    when /^start(_|-)?and(_|-)?stop$/i,
         '1+2',
         /^start(_|-)?stop$/i,
         'stopandstart',
         'yin_yang',
         '+-'
      show_start_and_stop_codons
    # ===================================================================== #
    # === stop_extended?
    # ===================================================================== #
    when 'stop_extended?'
      _ = main_sequence?
      stop_codons?.each {|this_stop_codon|
        _splitted = _.split(/#{this_stop_codon}/).each {|line|
          erev line+orange(this_stop_codon)+rev
        }
      }
      pp _splitted
    # ===================================================================== #
    # === rf "Horseradish Peroxidase"
    # ===================================================================== #
    when /^Horseradish(-|_)Peroxidase$/i
      show_resources_about_the_horseradish_peroxidase
    # ===================================================================== #
    # === mimivirus?
    # ===================================================================== #
    when /^mimivirus\??$/,'mimi'
      e 'Accession number is: '+
         sfancy('NC_014649')
    # ===================================================================== #
    # === user_input?
    #
    # This entry point is mostly used for debugging purposes.
    # ===================================================================== #
    when /^user(_|-)?input\??$/i
      pp @internal_hash[:user_input]
    # ===================================================================== #
    # === nls?
    # ===================================================================== #
    when 'nls?',
         'show_known_nls_sequences',
         'showknownnlssequences'
      show_known_nls_sequences
    # ===================================================================== #
    # === reste?
    # ===================================================================== #
    when 'reste?','show_reste','showreste','sreste'
      show_reste
    # ===================================================================== #
    # === test_colour_scheme
    # ===================================================================== #
    when /^test(_|-)?colour(_|-)?scheme$/i,
         'test_random_scheme'
      _ = random_dna_sequence
      colour_scheme_for_nucleotides(_)
    # ===================================================================== #
    # === compare_two_strings_as_alignment
    # ===================================================================== #
    when /compare_?two_?strings_?as_?alignment/i,'sstring','scompare',
         'sscompare','compare_two_strings','compare',
         /string_?compare/
      compare_two_strings_as_alignment(
        first_argument, second_argument
      ) # string_compare
    # ===================================================================== #
    # === left_chop
    #
    # This entry point allows the user to perform a so-called
    # "left-chop operation", aka to trim away nucleotides
    # that are on the left hand side of the sequence.
    # ===================================================================== #
    when /left(_|-)?chop$/,
         /left(_|-)?remove$/,
         /chop(_|-)?first$/,
         'chop5',
         'lchop'
      left_chop(a?)
    # ===================================================================== #
    # === translate_aminoacid
    #
    # Usage example:
    #
    #   translate kkrnn
    #
    # ===================================================================== #
    when /translate(_|-| )?aminoacid/i,
         'transaa',
         'translate_aa',
         'aminosäuren2',
         'translateaa',
         'trans2'
      translate_aminoacid(a?)
    # ===================================================================== #
    # === chi_sequence?
    # ===================================================================== #
    when 'chi_sequence?','chisequence?','chi?'
      e 'The chi sequence goes: '+simp('GCTGGTGG')
    # ===================================================================== #
    # === ncbi
    # ===================================================================== #
    when 'ncbi' # ncbi arabidopsis thaliana CDKs
      open_this_ncbi_page(a?)
    # ===================================================================== #
    # === pcolour
    # ===================================================================== #
    when 'interactively_pick_colour',
         'pick_colour',
         'pickcolour',
         'pcolour',
         'pcolor',
         'pcol'
      interactively_pick_colour
    # ===================================================================== #
    # === bioroebe --gtk1
    #
    # This is for alignment.rb
    # ===================================================================== #
    when /^-?-?gtk1$/i
      require 'bioroebe/gui/gtk3/alignment/alignment.rb'
      Bioroebe::GUI::Gtk::Alignment.run
    # ===================================================================== #
    # === bioroebe --gtk2
    #
    # This is for aminoacid_composition.rb
    # ===================================================================== #
    when /^-?-?gtk2$/i
      require 'bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb'
      Bioroebe::GUI::Gtk::AminoacidComposition.run
    # ===================================================================== #
    # === bioroebe --gtk3
    #
    # This is for anti_sense_strand.rb
    # ===================================================================== #
    when /^-?-?gtk3$/i
      require 'bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb'
      Bioroebe::GUI::Gtk::AntiSenseStrand.run
    # ===================================================================== #
    # === bioroebe --gtk4
    #
    # This is for blosum_matrix_viewer.rb
    # ===================================================================== #
    when /^-?-?gtk4$/i
      require 'bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb'
      Bioroebe::GUI::Gtk::BlosumMatrixViewer.run
    # ===================================================================== #
    # === bioroebe --gtk5
    #
    # This is for calculate_cell_numbers_of_bacteria.rb
    # ===================================================================== #
    when /^-?-?gtk5$/i
      require 'bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb'
      Bioroebe::GUI::Gtk::CalculateCellNumbersOfBacteria.run
    # ===================================================================== #
    # === bioroebe --gtk6
    #
    # This is for dna_to_aminoacid_widget.rb
    # ===================================================================== #
    when /^-?-?gtk6$/i
      require 'bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
      Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run
    # ===================================================================== #
    # === bioroebe --gtk7
    #
    # This is for dna_to_reverse_complement_widget.rb
    # ===================================================================== #
    when /^-?-?gtk7$/i
      require 'bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb'
      Bioroebe::GUI::Gtk::DnaToReverseComplementWidget.run
    # ===================================================================== #
    # === bioroebe --gtk8
    #
    # This is for fasta_table_widget.rb
    # ===================================================================== #
    when /^-?-?gtk8$/i
      require 'bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb'
      Bioroebe::GUI::Gtk::FastaTableWidget.run
    # ===================================================================== #
    # === bioroebe --gtk9
    #
    # This is for format_converter.rb
    # ===================================================================== #
    when /^-?-?gtk9$/i
      require 'bioroebe/gui/gtk3/format_converter/format_converter.rb'
      Bioroebe::GUI::Gtk::FormatConverter.run
    # ===================================================================== #
    # === bioroebe --gtk10
    #
    # This is for gene.rb
    # ===================================================================== #
    when /^-?-?gtk10$/i
      require 'bioroebe/gui/gtk3/gene/gene.rb'
      Bioroebe::GUI::Gtk::Gene.run
    # ===================================================================== #
    # === bioroebe --gtk11
    #
    # This is for hamming_distance.rb.
    # ===================================================================== #
    when /^-?-?gtk11$/i
      require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
      Bioroebe::GUI::Gtk::HammingDistance.run
    # ===================================================================== #
    # === bioroebe --gtk12
    #
    # This is for levensthein_distance.rb.
    # ===================================================================== #
    when /^-?-?gtk12$/i,
         /^-?-?gtk(_|-| )?levensthein$/i # bioroebe --gtk-levensthein
      require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
      Bioroebe::GUI::Gtk::LevenstheinDistance.run
    # ===================================================================== #
    # === bioroebe --gtk13
    #
    # This is for notebook.rb.
    # ===================================================================== #
    when /^-?-?gtk13$/i
      require 'bioroebe/gui/gtk3/controller/controller.rb'
      Bioroebe::GUI::Gtk::Controller.run
    # ===================================================================== #
    # === bioroebe --gtk14
    #
    # This is for nucleotide_analyser.rb.
    # ===================================================================== #
    when /^-?-?gtk14$/i
      require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
      Bioroebe::GUI::Gtk::NucleotideAnalyser.run
    # ===================================================================== #
    # === bioroebe --gtk15
    #
    # This is for parse_pdb_file.rb.
    # ===================================================================== #
    when /^-?-?gtk15$/i
      require 'bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb'
      Bioroebe::GUI::Gtk::ParsePdbFile.run
    # ===================================================================== #
    # === bioroebe --gtk16
    #
    # This is for primer_design_widget.
    # ===================================================================== #
    when /^-?-?gtk16$/i,
         /^-?-?primer(_|-| )?design$/i # bioroebe --primer-design
      require 'bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb'
      Bioroebe::GUI::Gtk::PrimerDesignWidget.run
    # ===================================================================== #
    # === bioroebe --gtk17
    #
    # This is for protein_to_DNA.
    # ===================================================================== #
    when /^-?-?gtk17$/i
      require 'bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb'
      Bioroebe::GUI::Gtk::ProteinToDNA.run
    # ===================================================================== #
    # === bioroebe --gtk18
    #
    # This is for random_sequence.
    # ===================================================================== #
    when /^-?-?gtk18$/i
      require 'bioroebe/gui/gtk3/random_sequence/random_sequence.rb'
      Bioroebe::GUI::Gtk::RandomSequence.run
    # ===================================================================== #
    # === bioroebe --gtk19
    #
    # This is for restriction_enzymes.
    # ===================================================================== #
    when /^-?-?gtk19$/i
      require 'bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb'
      Bioroebe::GUI::Gtk::RestrictionEnzymes.run
    # ===================================================================== #
    # === bioroebe --gtk20
    #
    # This is for show_codon_table.
    # ===================================================================== #
    when /^-?-?gtk20$/i
      require 'bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb'
      Bioroebe::GUI::Gtk::ShowCodonTable.run
    # ===================================================================== #
    # === at_content?
    #
    # Usage example:
    #
    #   at_content? AGTACGTACGTCAGTCA
    #
    # ===================================================================== #
    when /^at_?content\??$/i,
         'at?',
         'calc_at_content',
         'calcatcontent'
      calculcate_at_content(a?)
    # ===================================================================== #
    # === ll
    #
    # This is the general entry point for listing the content in the
    # current working directory.
    # ===================================================================== #
    when 'll',
         'ls',
         'l',
         'sdc',
         'lll',
         'llll',
         /^show(_|-)?file(_|-)?listing$/
      show_file_listing
    # ===================================================================== #
    # === remove
    #
    # This entry point can be used to remove a subsequence from the
    # 5' end (the "left" end).
    #
    # Invocation example:
    #
    #   remove 3
    #
    # ===================================================================== #
    when 'remove',
         'delete',
         'del',
         'rm'
      remove(a?)
    # ===================================================================== #
    # === oligo_two
    # ===================================================================== #
    when 'oligo_two',
         'oligo_length_two',
         'oligolengthtwo',
         'two',
         'oligonucleotide_frequency'
      show_oligo_length_two
    # ===================================================================== #
    # === efetch
    # ===================================================================== #
    when /^efetch$/
      efetch(a?)
    # ===================================================================== #
    # === Handle aminoacid sequence
    #
    # This is similar to the variant above, but it will work on the
    # aminoacid sequence. This explains the leading "aa", which
    # is short for "aminoacid".
    #
    # Usage example:
    #
    #   setdna 99; aa22..44
    #
    # ===================================================================== #
    when /^aa\[?([0-9,.]{0,9}\d{1,9})\s*[-.,]{1,4}\s*([0-9,.]{1,9})\]?$/
      show_this_subsequence($1, $2, aminoacid_sequence?)
    # ===================================================================== #
    # === gui_restriction_enzymes
    # ===================================================================== #
    when 'gui_restriction_enzymes','guirestrictionenzymes'
      enable_gtk
      ::Bioroebe::RestrictionEnzymes.start_gui_application
    # ===================================================================== #
    # === 2
    # ===================================================================== #
    when '2','restriction_enzymes','2_restriction_enzymes_run'
      load_gtk
      thread = Thread.new { restriction_enzymes_run }
      thread.join
    # ===================================================================== #
    # === bioroebe --hamming-gui
    # ===================================================================== #
    when /^-?-?hamming(_|-| )?gui$/i
      require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
      Thread.new {
        Bioroebe::GUI::Gtk::HammingDistance.run
      }
    # ===================================================================== #
    # === bioroebe --gtk-sizeseq
    # ===================================================================== #
    when /^-?-?gtk(_|-| )?sizeseq$/i
      require 'bioroebe/gui/gtk3/sizeseq/sizeseq.rb'
      Bioroebe::GUI::Gtk::Sizeseq.run
    # ===================================================================== #
    # === bioroebe --gtk-hamming
    # ===================================================================== #
    when /^-?-?gtk(_|-| )?hamming$/i
      require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
      Bioroebe::GUI::Gtk::HammingDistance.run
    # ===================================================================== #
    # === pwd
    # ===================================================================== #
    when 'pwd',
         'pdw',
         /^report(_|-)?current(_|-)?working(_|-)?directory$/i
      report_current_working_directory
    # ===================================================================== #
    # === restriction_table?
    # ===================================================================== #
    when /^restriction(_|-)?table\??/,
         /^show(_|-)?restriction(_|-)?table$/
      show_restriction_table
    # ===================================================================== #
    # === dna_weight?
    # ===================================================================== #
    when /dna_?weight\??/,'weight_of_dna_string',
         'weight?',
         'weight',
         'mweight',
         'show_and_calculate_weight_of_dna_string',
         'molwt',
         'show_individual_weight_of_the_four_dna_nucleotides'
      show_and_calculate_weight_of_dna_string_or_aminoacid_sequence(f)
    # ===================================================================== #
    # === dna_analyze?
    #
    # This entry-point can be used to analyze the given DNA strand at hand.
    # ===================================================================== #
    when 'dna_analyze?',
         'analyse',
         'ana',
         /^stats\??$/i,
         'display',
         'stat?',
         'stat',
         'dnaanalyze?',
         'frequencies',
         'frequencies?',
         'statistics?',
         'analyze_dna_string',
         'frequency',
         'superanalyze',
         /^dna(-|_| )?analyse$/i
      analyze_dna_string(a?)
    # ===================================================================== #
    # === tologdir
    # ===================================================================== #
    when /^to(_|-)?log(_|-)?dir$/,
         /^to(_|-)?log$/
      cd log_dir?
    # ===================================================================== #
    # === create_file
    #
    # This entry point allows the user to create a new file.
    # ===================================================================== #
    when /^create(_|-)?file$/,
         'touch'
      create_file(a?)
    # ===================================================================== #
    # === assign_aa
    # ===================================================================== #
    when /^assign(_|-)?aa$/,
         'aaa'
      assign_aminoacid_sequence(a?)
    # ===================================================================== #
    # === --create-jar
    # ===================================================================== #
    when /^-?-?create(_|-)?jar$/i,
         /^-?-?jar$/i
      ::Bioroebe.create_jar_archive
    # ===================================================================== #
    # === help
    # ===================================================================== #
    when 'hel',
         'he','showhelp',
         /^-?-?help$/i,
         'hep',
         'hepl','elp',
         'show_help',
         '?',
         'hlep' # 'h' is reserved already.
      show_help(f)
    # ===================================================================== #
    # === bioroebe --gtk21
    #
    # This is for show_codon_usage.
    # ===================================================================== #
    when /^-?-?gtk21$/i
      require 'bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb'
      Bioroebe::GUI::Gtk::ShowCodonUsage.run
    # ===================================================================== #
    # === bioroebe --gtk22
    #
    # This is for sizeseq.
    # ===================================================================== #
    when /^-?-?gtk22$/i
      require 'bioroebe/gui/gtk3/sizeseq/sizeseq.rb'
      Bioroebe::GUI::Gtk::Sizeseq.run
    # ===================================================================== #
    # === bioroebe --gtk23
    #
    # This is for three_to_one.
    # ===================================================================== #
    when /^-?-?gtk23$/i
      require 'bioroebe/gui/gtk3/three_to_one/three_to_one.rb'
      Bioroebe::GUI::Gtk::ThreeToOne.run
    # ===================================================================== #
    # === bioroebe --gtk24
    #
    # This is for www_finder.
    # ===================================================================== #
    when /^-?-?gtk24$/i
      require 'bioroebe/gui/gtk3/www_finder/www_finder.rb'
      Bioroebe::GUI::Gtk::WwwFinder.run
    # ===================================================================== #
    # === gtk3
    # ===================================================================== #
    when 'gtk3',
         'load_gtk_subsection'
      load_gtk
      enable_gtk_section_antisensestrand
    # ===================================================================== #
    # === enable_gtk_section_antisensestrand
    # ===================================================================== #
    when /^enable(_|-)?gtk(_|-)?section(_|-)?antisensestrand$/
      enable_gtk_section_antisensestrand
    # ===================================================================== #
    # === enable_gtk
    # ===================================================================== #
    when /^-?-?enable(_|-)?gtk$/,
         'gtk'
      enable_gtk
    # ===================================================================== #
    # === codon_to_aminoacid
    # ===================================================================== #
    when /^codon(_|-)?to(_|-)?aminoacid$/
      e codon_to_aminoacid(a?)
    # ===================================================================== #
    # === toggle2
    # ===================================================================== #
    when 'toggle2'
      toggle_mode
    # ===================================================================== #
    # === name?
    # ===================================================================== #
    when 'name?',
         /^-?-?show(_|-| )?name(_|-| )?of(_|-| )?the(_|-| )?gene$/i
      show_name_of_the_gene
    # ===================================================================== #
    # === show_memo
    # ===================================================================== #
    when /show_?mnemo/,'mnemo','memo',
         'show_memo',
         'memo?'
      show_mnemo
    # ===================================================================== #
    # === bioroebe --gtk-nucleotide-analyser
    # ===================================================================== #
    when /^-?-?gtk(_|-| )?nucleotide(_|-| )?analyser$/i,
         /^-?-?nucleotide(_|-| )?analyser(_|-| )?gtk$/i
      require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
      Bioroebe::GUI::Gtk::NucleotideAnalyser.run
    # ===================================================================== #
    # === download_fasta
    # ===================================================================== #
    when /^download(_|-| )?fasta$/i,
         'dfasta',
         'dfa',
         'wget'
      download_fasta(a?)
    # ===================================================================== #
    # === Handle 33..55 and 33-55 and [33..55] and [33-55]
    #
    # This entry point can be used to obtain a subsequence of our target
    # sequence - it can "handle ranges".
    #
    # See the following link for an explanation of this regex:
    #
    #   https://rubular.com/r/zP7khUUIyC3zA0
    #
    # ===================================================================== #
    when /^\[?([0-9,.]{0,9}\d{1,9})\s*[-.,]{1,4}\s*([0-9,.]{1,9})\]?$/
      show_this_subsequence($1, $2)
    # ===================================================================== #
    # === blosum90
    # ===================================================================== #
    when /^-?-?blosum90/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === calculate_levensthein
    # ===================================================================== #
    when /calculate(_|-| )?levensthein(_|-| )?distance/i,
         'calculate_levensthein' # lst computation complication
      ::Bioroebe.calculate_levensthein_distance(a?) # This will output the result by default.
    # ===================================================================== #
    # === longest_substring
    # ===================================================================== #
    when /longest(_|-)?substring/,
         'find_substring',
         'substring',
         'sub'
      find_longest_substring(a?) # sub AAAAGATAAACAAAAGGGG ATATCCTAAACAAAAGGGG
    # ===================================================================== #
    # === set_xclip
    # ===================================================================== #
    when /^set(_|-)?xclip$/i,
         'set_buffer',
         'xclip',
         'buffer',
         /^to(_|-)?buffer/i,
         'xorgbuffer',
         'setxorg'
      erev 'Next assigning the main DNA sequence to the Xorg Buffer.'
      set_xclip
    # ===================================================================== #
    # === to_base
    # ===================================================================== #
    when /to(_|-)?base$/,
         'base',
         /enter_?base_?dir/
      enter_base_directory
    # ===================================================================== #
    # === three_to_one
    #
    # This entry point will convert the three-letter code to the
    # one-letter code (in regards to aminoacids).
    #
    # Invocation example:
    #
    #   3to1 ARG-ALA-SER-LEU-PHE-TRP-LYS-HIS-ASN-SER-VAL-LEU-ILE-VAL-PRO
    #
    # ===================================================================== #
    when /^three(_|-)?to(_|-)?one$/,
         '3-1',
         '3letters',
         /^3(_|-| )?to(_|-| )?1$/ # === 3to1
      three_to_one(a?)
    # ===================================================================== #
    # === oligo_three
    # ===================================================================== #
    when /^oligo(_|-)?three$/,
         'oligo_length_three',
         'oligolengththree',
         'three',
         /^show(_|-)?oligo(_|-)?length(_|-)?three$/,
         'oligo_3',
         'oligo3'
      show_oligo_length_three
    # ===================================================================== #
    # === random_insert
    # ===================================================================== #
    when /^random(_|-)?insert$/i,
         'rinsert'
      random_insert(a?)
    # ===================================================================== #
    # === 9cut
    # ===================================================================== #
    when /^\d+cut$/,
         /^cut\d+$/, # Example: "9cut" or "cut9".
         /^cut(_|-)?sequence(_|-)?in(_|-)?slices(_|-)?of$/i
      _ = f.to_s.gsub(/cut/,'')
      cut_sequence_in_slices_of(_)
    # ===================================================================== #
    # === runmode?
    # ===================================================================== #
    when /runmode?/
      e runmode?
    # ===================================================================== #
    # === subseq2
    #
    # Usage example:
    #
    #   set_raw_sequence ATGCATGCAAA; subseq2
    #
    # ===================================================================== #
    when /^-?-?subseq2$/i
      show_this_subsequence(2, 4, raw_sequence?)
      # ===================================================================== #
      # === set_raw_sequence
      #
      # Usage example:
      #
      #   set_raw_sequence ATGCATGCAAA; raw_sequence?
      #   setrawsequence ATGCATGCAAA; raw_sequence?
      #
      # ===================================================================== #
    when /^-?-?set(_|-| )?raw(_|-| )?sequence$/i,
         /^-?-?assign(_|-| )?raw$/i
      erev 'Now assigning to the new sequence '+sfancy(f)
      set_raw_sequence(f)
    # ===================================================================== #
    # === annotate
    # ===================================================================== #
    when 'annotate'
      annotate_this_file(f)
    # ===================================================================== #
    # === hydropathy_table?
    # ===================================================================== #
    when 'hydropathy_table?',
         'hydropathytable?',
         'show_hydropathy_table',
         'showhydropathytable',
         'hydropathy?',
         /hpathy\??/,
         'spathy',
         'hydropathy_table',
         'hytable'
      show_hydropathy_table
    # ===================================================================== #
    # === restriction_sizes
    # ===================================================================== #
    when /^restriction(_|-)?sites$/i,
         'rest',
         'restriction',
         'sites',
         'res',
         'show_restriction_enzymes',
         'enzymes',
         'enz',
         'enzymes?',
         'rest2',
         'r',
         '4',
         'srest',
         'allrest',
         'show_rests'
      show_restriction_enzymes(:show_all) unless f
      find_restriction_sites(f) if f # Only do this if an argument was passed.
      @internal_hash[:bioroebe] << a.upcase if a
      @internal_hash[:bioroebe].restriction_sites?(dna_sequence?)
    # ===================================================================== #
    # === do_not_show_the_leader
    # ===================================================================== #
    when /^-?-?do_?not_?show_?the_?leader$/i,
         /^-?-?no_?leader$/i
      do_not_show_the_leader
    # ===================================================================== #
    # === readline?
    # ===================================================================== #
    when 'readline?'
      report_whether_readline_is_available
    # ===================================================================== #
    # === iaminoacid?
    # ===================================================================== #
    when 'iaminoacid?',
         /^identify(_|-)?aminoacid$/i,
         'iaminoacid',
         'aminoacid'
      identify_aminoacid(a?)
    # ===================================================================== #
    # === kozak?
    # ===================================================================== #
    when /^kozak\??$/i
      e
      erev '  GCCACCAUGG'
      e
    # ===================================================================== #
    # === first_atg?
    #
    # This entry point will show where the first ATG can be found in a
    # given sequence.
    # ===================================================================== #
    when /^first(_|-)?atg\??/i,
         /^report(_|-)?the(_|-)?first(_|-)?atg$/i
      report_the_first_atg
    # ===================================================================== #
    # === insulin
    #
    # This quick-link is used mostly just to quickly jump to the
    # insulin sequence.
    # ===================================================================== #
    when 'insulin'
      _ = NCBI_NUCCORE+'NC_000011.10?report=fasta&from=2159779&to=2161209&strand=true'
      e _
      open_in_browser _
    # ===================================================================== #
    # === Handle numbers given as input
    #
    # This entry point can be used to match numbers, such as 33 or
    # 66.
    # ===================================================================== #
    when /^[0-9]+$/
      assign(i)
    # ===================================================================== #
    # === assign_protein
    # ===================================================================== #
    when /^assign(_|-)?protein$/,
         /^assign(_|-)?aminoacids$/,
         'aprotein'
      assign_protein_sequence(a?)
    # ===================================================================== #
    # === show_complement
    # ===================================================================== #
    when 'show_complement',
         'complement',
         'complement?',
         'complementary',
         'cment',
         'c?',
         'co',
         'clent',
         'compl',
         'partner'
      show_complement(all_arguments?, :show_leading_primes)
    # ===================================================================== #
    # === ensure_that_the_base_directories_exist
    # ===================================================================== #
    when /^ensure(_|-)?that(_|-)?the(_|-)?base(_|-)?directories(_|-)?exist$/i
      erev 'Now creating some '+steelblue('base directories')+rev+
           ' for the bioroebe project.'
      Bioroebe.ensure_that_the_base_directories_exist
    # ===================================================================== #
    # === sizeseq
    # ===================================================================== #
    when /sizeseq/
      run_sizeseq
    # ===================================================================== #
    # === frame123
    # ===================================================================== #
    when 'frame123'
      showorf(dna_sequence?, :frame1_frame2_frame3)
    # ===================================================================== #
    # === find_restriction_sites
    # ===================================================================== #
    when 'find_restriction_sites',
         'rest?',
         'findrestrictionsites'
      find_restriction_sites(string?)
    # ===================================================================== #
    # === 1mbo
    # ===================================================================== #
    when /^1mbo$/
      download_this_pdb_file('1mbo')
    # ===================================================================== #
    # === no_truncate
    # ===================================================================== #
    when /^dont(_|-)?truncate$/,
         'do_not_truncate',
         'donottruncate',
         'no_truncate',
         'notruncate',
         'truncate-',
         '-truncate',
         '-trunc'
      do_not_truncate
    # ===================================================================== #
    # === pstop
    # ===================================================================== #
    when 'pstop',
         'astop'
      append_stop_codon
    # ===================================================================== #
    # === create_fasta
    # ===================================================================== #
    when /^create(_|-)?fasta$/i,
         /^make(_|-)?fasta$/i,
         /^save(_|-)?fasta$/i,
         /^create_?fasta_?file/
      create_fasta_file
    # ===================================================================== #
    # === K12
    # ===================================================================== #
    when 'K12'
      show_Ecoli_K12_information
    # ===================================================================== #
    # === test10
    # ===================================================================== #
    when 'test10'
      # =================================================================== #
      # Just some testing here.
      # =================================================================== #
      dna = ::Bioroebe::DNA.new(string?)
      find_this_subsequence = 'ATG'
      e 'Looking for '+royalblue(find_this_subsequence)
      array = dna.find_this_subsequence find_this_subsequence
      pp array
    # ===================================================================== #
    # === atgccontent
    # ===================================================================== #
    when 'atgccontent',
         'atcgcontent',
         'ncontent',
         'tacgcontent'
      calculcate_at_content(a?)
      calculcate_gc_content(a?)
    # ===================================================================== #
    # === use_fasta
    # ===================================================================== #
    when /^use_?fasta$/i,
         'use_this_fasta',
         'ufasta',
         'usethisfasta',
         'use_this_fasta_file',
         'useasta'
      use_this_fasta_file(f) # Use a fasta file based on its position.
    # ===================================================================== #
    # === The ViennaRNA package
    # ===================================================================== #
    when 'b2ct',
         'ct2db',
         'Kinfold',
         'popt',
         'RNA2Dfold',
         'RNAaliduplex',
         'RNAalifold',
         'RNAcofold',
         'RNAdistance',
         'RNAduplex',
         'RNAeval',
         'RNAfold',
         'RNAforester',
         'RNAheat',
         'RNAinverse',
         'RNALalifold',
         'RNALfold',
         'RNAlocmin',
         'RNApaln',
         'RNAparconv',
         'RNApdist',
         'RNAPKplex',
         'RNAplex',
         'RNAplfold',
         'RNAplot',
         'RNApvmin',
         'RNAsnoop',
         'RNAsubopt',
         'RNAup'
      this_command = i.dup+' '
      if a
        this_command << a.join(' ').chomp
      end
      e
      esystem(this_command)
      e
    # ===================================================================== #
    # === restore
    #
    # This will restore the last chop-operation.
    # ===================================================================== #
    when 'restore'
      restore_the_last_chop_operation
    # ===================================================================== #
    # === mirror_repeat
    # ===================================================================== #
    when /^mirror(_|-)?repeat$/i,
         /^mirror$/i
      mirror_repeat(a?)
    # ===================================================================== #
    # === TTAA
    # ===================================================================== #
    when 'TTAA?',
         'TTAA',
         'TTA_transposon'
      show_colourized_sequence('TTAA')
    # ===================================================================== #
    # === count_nucleotides
    # ===================================================================== #
    when 'cnucleotides',
         /count_?nucleotides/
      ::Bioroebe::CountAmountOfNucleotides.new(f) # cnucleotides ATTGGCTTGCCGGCAGACGA
    # ===================================================================== #
    # === all_sequences?
    # ===================================================================== #
    when 'all_sequences?',
         'allsequences?'
      show_main_dna_sequence # We show them only when they are NOT empty.
      show_seq_2 unless seq2?.empty?
      show_seq_3 unless seq3?.empty?
      show_seq_4 unless seq4?.empty?
      show_seq_5 unless seq5?.empty?
      show_seq_6 unless seq6?.empty?
    # ===================================================================== #
    # === CAP?
    # ===================================================================== #
    when 'CAP?',
         'CAP',
         'cap',
         'cap?'
      try_to_find_restriction_enzymes_for('TGTGA') # See: http://www.jbc.org/content/261/23/10885.full.pdf
    # ===================================================================== #
    # === unfreeze
    # ===================================================================== #
    when /^unfreeze$/,
         /^unfrozen$/,
         /^unfreeze(-|_| )?the(-|_| )?main(-|_| )?sequence$/
      erev 'Unfreezing the main sequence next.'
      unfreeze_the_main_sequence
    # ===================================================================== #
    # === show_editor_in_use
    # ===================================================================== #
    when /^show(_|-)?editor(_|-)?in(_|-)?use$/,
         'editor?',
         'ed?'
      show_editor_in_use
    # ===================================================================== #
    # === Mus_musculus.GRCm38.75.gtf.gz
    # ===================================================================== #
    when 'Mus_musculus.GRCm38.75.gtf.gz'
      download(
        'ftp://ftp.ensembl.org/pub/release-75/gtf/mus_musculus/Mus_musculus.GRCm38.75.gtf.gz'
      )
    # ===================================================================== #
    # === dump
    # ===================================================================== #
    when /^dump$/i
      dump(a?)
    # ===================================================================== #
    # === seq2?
    # ===================================================================== #
    when 'seq2?',
         's2?',
         /^show_?seq_?2/
      show_seq_2
    # ===================================================================== #
    # === seq2
    # ===================================================================== #
    when 'seq2'
      assign_sequence2(a?)
    # ===================================================================== #
    # === index_this_fasta_file
    #
    # This entry point will use samtools to index .fasta file(s).
    #
    # If no argument is given then this method will, by default, try
    # to use all .fasta and .fa files from the current working
    # directory. This feature exists primarily for convenience.
    # ===================================================================== #
    when /^-?-?index(_|-)?this(_|-)?fasta(_|-)?file$/i,
         /^-?-?index$/i
      index_this_fasta_file(a?) { :use_all_fasta_files_if_no_argument_was_given }
    # ===================================================================== #
    # === sanitize_nucleotide_sequence
    # ===================================================================== #
    when /^sanitize(_|-)?nucleotide(_|-)?sequence$/
      sanitize_nucleotide_sequence(a?)
    # ===================================================================== #
    # === align_ORFS
    # ===================================================================== #
    when /^align_?ORFS/i,'alignmorfs',
          'pretty_orf',
         /^align_?open_?reading_?frames/
      align_ORFS # Show all ORFs properly aligned.
    # ===================================================================== #
    # === pcr?
    # ===================================================================== #
    when 'pcr?'
      calculate_melting_temperature :show_formulas
    # ===================================================================== #
    # === completions?
    # ===================================================================== #
    when 'completions?','complet?'
      if use_readline?
        show_readline_completions
      else
        erev 'No completions are known, as the readline '\
             'module is not in use.'
      end
    # ===================================================================== #
    # === phred_quality_score_table
    # ===================================================================== #
    when /phred(_|-)?quality(_|-)?score(_|-)?table/
      require 'bioroebe/ngs/phred_quality_score_table.rb'
      ::Bioroebe::PhredQualityScoreTable.new
    # ===================================================================== #
    # === cuts_at?
    #
    # Where restriction enzymes cut.
    # ===================================================================== #
    when 'cuts_at?',
         'cuts_at',
         'cut?',
         'r?',
         'find_restriction_enzymes_that_cut_at',
         'findcutat?',
         'cutsat?'
      find_restriction_enzymes_that_cut_at(a?)
    # ===================================================================== #
    # === delimiter
    # ===================================================================== #
    when /delimiter/
      show_sequence_in_splitted_form(f) {{ use_this_token: '|' }}
    # ===================================================================== #
    # === aaruler
    #
    # Usage example:
    #
    #   aaruler KLKLKLKLAALKLAKLA
    #
    # ===================================================================== #
    when /^aaruler$/
      _ = aminoacid_sequence? # Default value.
      if f and !f.nil? and !f.empty?
        _ = f
      end
      show_sequence_with_a_ruler(:default, _, :aminoacids)
    # ===================================================================== #
    # === ruler
    #
    # This entry point will display a useful number on each nucleotide
    # position.
    # ===================================================================== #
    when /^ruler$/,
         /^-?-?show(_|-| )?sequence(_|-| )?with(_|-| )?a(_|-| )?ruler$/
      show_sequence_with_a_ruler(a?, :default, :dna)
    # ===================================================================== #
    # === e
    #
    # This entry point can be used to quickly feedback which arguments
    # have been passed.
    #
    # Specific usage example:
    #
    #   e one two three
    #
    # ===================================================================== #
    when 'e'
      e all_arguments?
    # ===================================================================== #
    # === check_for_mismatches
    # ===================================================================== #
    when /^check(_|-)?for(_|-)?mismatches$/i,
         'mismatch',
         'mismatches'
      check_for_mismatches
    # ===================================================================== #
    # === bedtoolsv
    # ===================================================================== #
    when 'bedtoolsv',
         'bedtools?',
         /^try(_|-)?to(_|-)?report(_|-)?the(_|-)?version(_|-)?of(_|-)?bedtools$/
      try_to_report_the_version_of_bedtools
    # ===================================================================== #
    # === return_random_nucleotide
    # ===================================================================== #
    when /^return(_|-)?random(_|-)?nucleotide$/i
      e return_random_nucleotide
    # ===================================================================== #
    # === return_random_aminoacid
    # ===================================================================== #
    when /^return(_|-)?random(_|-)?aminoacid$/i
      e return_random_aminoacid
    # ===================================================================== #
    # === cut_with_enzyme
    #
    # This entry point can be used to cut a DNA sequence with a
    # restriction enzyme.
    #
    # Invocation example:
    #
    #   cut_with_enzyme EcoRI
    #
    # ===================================================================== #
    when /^cut(_|-)?with(_|-)?enzyme$/i
      cut_with_enzyme(a?)
    # ===================================================================== #
    # === show_history
    #
    # This entry point can be used to show the input-history that was
    # used so far. The "input-history" is what the user typed.
    # ===================================================================== #
    when /^show(_|-)?history$/i,
         'h',
         'h?',
         'history',
         'history?',
         'hist',
         'hist?'
      show_history
    # ===================================================================== #
    # === try_to_find_this_restriction_enzyme
    # ===================================================================== #
    when /^try(_|-)?to(_|-)?find(_|-)?this(_|-)?restriction(_|-)?enzyme$/
      try_to_find_this_restriction_enzyme(f)
    # ===================================================================== #
    # === dalton
    # ===================================================================== #
    when /^dalton$/i
      dalton(f?)
    # ===================================================================== #
    # === search_for
    # ===================================================================== #
    when /^search(_|-)?for$/ 
      search_for(a?)
    # ===================================================================== #
    # === colour_test
    # ===================================================================== #
    when /^colour(_|-)?test$/i
      set_highlight_colour(:violet)
    # ===================================================================== #
    # === to_dna
    # ===================================================================== #
    when /^to(_|-| )?DNA$/i,
         'dna',
         'rna2dna'
      to_dna(f)
    # ===================================================================== #
    # === backtranseq
    #
    # This entry point allows us to translate an Aminoacid Sequence back
    # into the most likely DNA sequence.
    #
    # Usage example:
    #
    #   backtranseq ARGARG
    #
    # ===================================================================== #
    when 'backtranseq',
         'backseq',
         'backtrack',
         /^aminoacid(_|-| )?to(_|-| )?dna$/i,
         'runcodons',
         'btrack',
         /^protein(_|-| )?to(_|-| )?dna$/i,
         'proteintodna',
         'p_to_d','ptod',
         /^reverse(_|-| )?dna$/i,
         /^reverse(_|-| )?seq$/i,
         /^reverse(_|-| )?aa$/i, # === reverse_aa
         'bseq',
         'backtraq',
         'backtrach'
      backtranseq(a?)
    # ===================================================================== #
    # === colour_test
    # ===================================================================== #
    when /^colour(_|-)?test/
      e
      erev 'This is a test.'
      e
      erev 'This is another test.'
      erev 'Now for '+slateblue('slateblue')+rev+'.'
      erev 'Now for '+lightgreen('lightgreen')+rev+'.'
      e
    # ===================================================================== #
    # === show_aminoacids_mass_table
    # ===================================================================== #
    when /^show(_|-)?aminoacids(_|-)?mass(_|-)?table$/i,
         /^show(_|-)?aminoacid(_|-)?mass$/i,
         'showmass',
         'aminoacid_table_overview',
         'aminomass',
         'aminomasses'
      show_aminoacids_mass_table
    # ===================================================================== #
    # === stride
    # ===================================================================== #
    when 'stride' # The C-program called stride.
      _ = 'stride '+f?.to_s+' > '+f?.to_s+'_stride_output'
      esystem(_)
    # ===================================================================== #
    # === multliline_assignment
    # ===================================================================== #
    when /^multiline_?assignment$/,
         'mass',
         'multiline2',
         'mline',
         'mmm',
         '___',
         '__',
         '--',
         'assignmultiline',
         'assign_multiline',
         'multiline_input',
         'multilineinput',
         'multi_line',
         'multiline',
         'multi-line',
         'multi_input',
         'multline'
      assign_sequence(:multiline)
    # ===================================================================== #
    # === download_dir?
    # ===================================================================== #
    when /^download(_|-)?dir\??$/,
         'ddir?','base?',
         'depotdir?','depot?',
         /^temp\??$/i,
         /^show(_|-)?download(_|-)?dir$/ # === show_download_dir
      show_download_dir
    # ===================================================================== #
    # === @parse_fasta
    # ===================================================================== #
    when '@parse_fasta'
      last_fasta_entry?.display
    # ===================================================================== #
    # === show_aa
    # ===================================================================== #
    when /^show(_|-)?aa$/i,
         'aminoacids?','aaseq?','aasq?','aminacids?',
         'aminocids?',
         'aasequence?',
         /^show(_|-)?aminoacid(_|-)?sequence$/i
      show_aminoacid_sequence
    # ===================================================================== #
    # === pyrrolysine
    # ===================================================================== #
    when /pyrrolysine?\??/
      erev 'UAG codes for pyrrolysine'
    # ===================================================================== #
    # === to_T
    #
    # Convert all 'U' into 'T', if there are any U at all.
    # ===================================================================== #
    when /^to(_|-)?T$/i
      dna_sequence_object?.extend(Bioroebe::NucleotideModule)
      assign_this_dna_sequence(
        dna_sequence_object?.to_T
      )
    # ===================================================================== #
    # === theory?
    # ===================================================================== #
    when 'theory','theory?'
      e '  T = h ** 2 + h*k + k ** 2'
    # ===================================================================== #
    # === ..
    # ===================================================================== #
    when '..'
      cd '..'
    # ===================================================================== #
    # === last_inputted_command?
    # ===================================================================== #
    when /^last(_|-)?inputted(_|-)?command\??$/i
      e last_inputted_command?
    # ===================================================================== #
    # === flybase?
    # ===================================================================== #
    when /^flybase\??$/i
      open_in_browser(i.delete('?'))
    # ===================================================================== #
    # === fasta_file?
    # ===================================================================== #
    when /^fasta(_|-)?file\??$/i
      e fasta_file?
    # ===================================================================== #
    # === dna?
    # ===================================================================== #
    when 'dnaa?',
         'dnaA',
         'dnaA?'
      attempt_to_discover_dna_A_boxes
    # ===================================================================== #
    # === useful_packages?
    # ===================================================================== #
    when /^useful(_|-)?packages\??$/,
         /^science(_|-)?addons\??$/,
         /^addons\??$/,
         /^external\??$/,
         /^status\??$/,
         /^report$/
      report_useful_packages_installed
    # ===================================================================== #
    # === f23
    # ===================================================================== #
    when 'f2,f3','f23'
      showorf(dna_sequence?, :frame2_frame3)
    # ===================================================================== #
    # === f1,f2
    # ===================================================================== #
    when 'f1,f2','f12'
      showorf(dna_sequence?, :frame1_frame2)
    # ===================================================================== #
    # === f1,f2,f3
    # ===================================================================== #
    when 'f1,f2,f3'
      showorf(dna_sequence?, :frame1_frame2_frame3)
    # ===================================================================== #
    # === genbank?
    # ===================================================================== #
    when 'genbank?'
      open_in_browser :genbank
    # ===================================================================== #
    # === gold?
    # ===================================================================== #
    when 'gold?'
      _ = 'https://gold.jgi.doe.gov/'
      e _
      open_in_browser(_)
    # ===================================================================== #
    # === purge
    # ===================================================================== #
    when 'purge'
      purge(a?)
    # ===================================================================== #
    # === restrictionenzymes?
    # ===================================================================== #
    when 'restrictionenzymes?','restrictionenzymes','restriction?'
      show_restriction_enzymes(:show_all)
    # ===================================================================== #
    # === longest_ORF
    # ===================================================================== #
    when /^longest(_|-| )?ORF$/i
      _ = Bioroebe.longest_ORF?(sequence_as_string?)
      erev 'The longest ORF has a size of '+steelblue(_.size.to_s)+
           rev+' nucleotides.'
      erev 'This sequence is shown next:'
      e
      show_this_sequence(_)
      e
    # ===================================================================== #
    # === codon_usage_database?
    # ===================================================================== #
    when /^codon(_|-)?usage(_|-)?database\??$/i
      erev 'On 20.05.2016 this database has had:'
      e
      erev '  35,799 organisms'
      erev "  3,027,973 complete protein coding genes (CDS's)"
      e
    # ===================================================================== #
    # === 1IGT
    #
    # This .pdb file is related to antibodies.
    # ===================================================================== #
    when '1IGT'
      open_1igt_in_the_browser
    # ===================================================================== #
    # === enable_xsel
    # ===================================================================== #
    when /^enable(_|-)?xsel$/i
      enable_xsel
    # ===================================================================== #
    # === show_xorg_buffer
    # ===================================================================== #
    when /^show(_|-)?xorg(_|-)?buffer$/i,
         /^show(_|-)?xbuffer$/i,
         'sxorgbuffer'
      show_xorg_buffer
    # ===================================================================== #
    # === weight_of_nucleotides
    #
    # This entry point simply shows the weight of the four different
    # nucleotides.
    # ===================================================================== #
    when /^weight(_|-)?of(_|-)?nucleotides$/i,
         /^wnuc$/i
      show_the_weight_of_the_four_individual_nucleotides
    # ===================================================================== #
    # === viennarnav
    # ===================================================================== #
    when /^viennarna(v|\?)?$/i # Allows both "viennarna" and "viennarna?"
      try_to_report_the_version_of_viennarna
    # ===================================================================== #
    # === yaml?
    # ===================================================================== #
    when 'yaml','yaml?',
         /^show(_|-)?all(_|-)?yaml(_|-)?files/i
      show_all_yaml_files
    # ===================================================================== #
    # === match_pattern
    #
    # Usage example:
    #
    #   match_pattern ACGTACGTAACG GTA
    #   match_pattern ATGTGACTACGACGCATATGACGTACGTAACG ATG
    # 
    # ===================================================================== #
    when /^match(_|-)?pattern$/i
      results = Bioroebe.return_array_of_sequence_matches(
        first_argument?, second_argument?
      )
      results.reverse.each {|position|
        show_this_sequence(
          first_argument?[(position-1) .. -1]
        )
      }
    # ===================================================================== #
    # === to_genbank
    #
    # This entry point can be used to convert the main DNA sequence to
    # the genbank format.
    # ===================================================================== #
    when /^to(_|-)?genbank$/,
         'togen',
         'filemaker',
         'format?',
         'genbeauty',
         'beauty2',
         'togenb',
         'genbank',
         'togenban',
         'genbankflatfilegen',
         'formatter',
         'pretty',
         'prettify',
         'beautify',
         'sanitize',
         /table_?formatter/
      to_genbank
    # ===================================================================== #
    # === last_update?
    #
    # This entry point notifies the user as to when the bioroebe project
    # was last updated.
    # ===================================================================== #
    when /^last(_|-)?update\??$/i
      report_when_the_bioroebe_project_was_last_updated
    # ===================================================================== #
    # === colour_scheme
    #
    # Usage example:
    #
    #   colour_scheme ATGACTCAGACACTAGCTAGCTAGCTAGACTACA
    #
    # ===================================================================== #
    when /^colour(_|-)?scheme$/i,
         /^colour(_|-)?scheme(_|-)?for(_|-)?nucleotides$/i,
         'cscheme'
      colour_scheme_for_nucleotides(a?)
    # ===================================================================== #
    # === constants?
    # ===================================================================== #
    when 'constants?'
      pp ::Bioroebe.constants.sort
    # ===================================================================== #
    # === config?
    # ===================================================================== #
    when 'config?',
         'configuration?',
         'con?',
         'show_config',
         'showconfig'
      try_to_show_the_configuration
    # ===================================================================== #
    # === swisss-prot?
    # ===================================================================== #
    when /swiss-?prot\??/,
         /report_?n_?proteins_?registered_?in_?swiss_?prot$/
      report_n_proteins_registered_in_swiss_prot
    # ===================================================================== #
    # === rubyversion
    #
    # The second line is for jruby specifically.
    # ===================================================================== #
    when /^ruby(_|-)?version/i
      e steelblue(RUBY_VERSION)
      if Object.const_defined?(:ENV_JAVA)
        erev 'Java version: '+
             steelblue(ENV_JAVA['java.version'].to_s)
      end
    # ===================================================================== #
    # === disable
    #
    # This entry point allows us to disable specific features, as far
    # as the BioRoebe shell is concerned.
    # ===================================================================== #
    when /^disable/,
         'no'
      disable(a?)
    # ===================================================================== #
    # === shine_dalgarno?
    # ===================================================================== #
    when 'shine_dalgarno?','shine?',
         'shine',
         'shine_dalgarno',
         'sd',
         'sd?',
         'find_shine_dalgarno_sequence',
         'sine'
      find_shine_dalgarno_sequence
    # ===================================================================== #
    # === random_dna_sequence
    #
    # This entry point will simply display the random DNA sequence,
    # the default length. Currently this is 250.
    # ===================================================================== #
    when /^random(_|-)?dna(_|-)?sequence$/i
      display_this_nucleotide_sequence(
        random_dna_sequence
      )
    # ===================================================================== #
    # === raw?
    # ===================================================================== #
    when 'raw?','raw'
      show_dna_string(
        dna_string?, :do_not_truncate_and_do_not_show_leader_and_trailer
      )
    # ===================================================================== #
    # === salt_adjusted_tm
    #
    # Entry point for calculating the salt-adjust Tm (melting temperature).
    #
    # Most useful for primers in the range of 18-25, give or take.
    # ===================================================================== #
    when /^salt(_|-)?adjusted(_|-)?tm$/,
         /^melting(_|-)?temperature2$/
      erev salt_adjusted_tm(a?)
    # ===================================================================== #
    # === melting_temperature?
    # ===================================================================== #
    when 'calculate_melting_temperature','calculatemeltingtemperature',
         'mt','melting_temperature','ctemp','tm','melting?',
         'melting_temperature?','melt',
         'cmelt','calmelt'
      calculate_melting_temperature(a?) # melting? GCCGCGGTTTCGGGA
    # ===================================================================== #
    # === translate3
    # ===================================================================== #
    when 'translate3','t','aminoacid?','trans1'
      translate(a?)
    # ===================================================================== #
    # === bioroebe --libui1
    #
    # All --libui entries should be sorted alphabetically in this
    # menu as well.
    # ===================================================================== #
    when /^-?-?libui1?$/i
      require 'bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
      Bioroebe::GUI::LibUI::DnaToAminoacidWidget.run
    # ===================================================================== #
    # === bioroebe --libui2
    # ===================================================================== #
    when /^-?-?libui2$/i
      require 'bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
      Bioroebe::GUI::LibUI::DnaToAminoacidWidget.run
    # ===================================================================== #
    # === bioroebe --libui3
    # ===================================================================== #
    when /^-?-?libui3$/i
      require 'bioroebe/gui/libui/random_sequence/random_sequence.rb'
      Bioroebe::GUI::LibUI::RandomSequence.run
    # ===================================================================== #
    # === show_taxid
    # ===================================================================== #
    when 'show_taxid','showtaxid','taxid?','taxid'
      show_taxid(a?)
    # ===================================================================== #
    # === ten_split
    # ===================================================================== #
    when /^ten(_|-)?split$/i
      show_sequence_in_splitted_form(10)
    # ===================================================================== #
    # === n_downloads?
    # ===================================================================== #
    when 'n_downloads?' # How often Bioroebe was downloaded.
      require 'bestgems'
      n_times = Bestgems.client.total_downloads(:bioroebe).values.first
      erev 'The Bioroebe project has been downloaded '+simp(n_times.to_s)+rev+' times.'
    # ===================================================================== #
    # === genbank_version?
    # ===================================================================== #
    when /genbank_?version\??/,'report_current_genbank_version',
         'top',
         'genebank?',
         'reportcurrentgenbankversion',
         'genbankversion?',
         'genbank_version',
         'current_genbank_version?',
         'current_genbank_version'
      report_current_genbank_version(:also_report_the_URL)
    # ===================================================================== #
    # === phosphorylation_sites?
    # ===================================================================== #
    when 'phosphorylation_sites?','psites?','phosphorylationsites?',
         'phosphorylationsites','psites','phosphorylation_site?',
         'phospho?','show_phosphorylation_sites','showphosphorylationsites',
         'p?','P',
         'phosphorylation',
         'P?'
      show_possible_phosphorylation_sites
    # ===================================================================== #
    # === pitch
    # ===================================================================== #
    when 'pitch','alpha_helix_pitch',
         'alphahelixpitch'
      show_length_of_alpha_helix(a?)
    # ===================================================================== #
    # === handle_pdb_files
    #
    # Invocation example:
    #
    #   handle_pdb_files http://www.rcsb.org/pdb/files/3O30.pdb
    #
    # ===================================================================== #
    when /^handle(_|-)?pdb(_|-)?files$/i,
         'pdb','pdb?',
         'download_pdb',
         'dpdb',
         'downloadpdb',
         /^download(_|-)?this(_|-)?pdb(_|-)?file$/i
      handle_pdb_files(a?)
    # ===================================================================== #
    # === pdburl?
    # ===================================================================== #
    when /pdb(_|-| )?url?/,
         'pdb2?'
      e 'https://www.wwpdb.org/'
    # ===================================================================== #
    # === freeze
    # ===================================================================== #
    when /^freeze$/,
         /^frozen$/,
         /^freeze(-|_| )?the(-|_| )?main(-|_| )?sequence$/
      erev 'Freezing the main sequence next.'
      freeze_the_main_sequence
    # ===================================================================== #
    # === parse
    #
    # This is the general-entry for parse-related activities in regards
    # to the bioshell-interface.
    #
    # Examples for files that are parsed include .pdb files and
    # .fasta files.
    # ===================================================================== #
    when 'parse',
         /^parse(_|-| )?this(_|-| )?pdb(_|-| )?file$/,
         /^parse(_|-| )?pdb(_|-| )?file$/,
         /^parse(_|-| )?pdb$/,
          'parse_fasta_format',
         /^parse(_|-| )?fasta$/,
         'pfasta',
         'pasta',
         'fasta',
         'fast',
         /^assign(_|-| )?fasta$/
      parse(a?)
    # ===================================================================== #
    # === cut_at
    # ===================================================================== #
    when /cut(_|-)?at$/i
      cut_at(f)
    # ===================================================================== #
    # === punnet
    # ===================================================================== #
    when 'punnet',
         'pun'
      punnet(a?) # bl $BIOROEBE/shell/shell.rb
    # ===================================================================== #
    # === stop_frame1?
    # ===================================================================== #
    when /^stop(_|-)?frame1\??$/i
      report_main_sequence(dna_sequence_as_string?, :stop_codon_in_frame1)
    # ===================================================================== #
    # === stop_frame2?
    # ===================================================================== #
    when /^stop(_|-)?frame2\??$/i
      report_main_sequence(dna_sequence_as_string?, :stop_codon_in_frame2)
    # ===================================================================== #
    # === stop_frame3?
    # ===================================================================== #
    when /^stop(_|-)?frame3\??$/i
      report_main_sequence(dna_sequence_as_string?, :stop_codon_in_frame3)
    # ===================================================================== #
    # === orf?
    #
    # This entry point will display to the user where open reading
    # frames can be found in the main sequence.
    # ===================================================================== #
    when /^ORF\??$/i,
         /^ORF1\??$/i,
         /^ORFs\??$/i,
         'open_reading_frames',
         'search?',
         'startcodons?',
         'search_for_orfs',
         'orfs?',
         /^open(_|-)?reading(_|-)?frames$/i,
         'start?',
         'toorf',
         'ORFS?',
         'all_ORFs',
         'allorfs',
         'ATG?',
         /^AUG\??$/i
      result = search_sequence_for_open_reading_frames
      print '  '
      pp result
      e
      # =================================================================== #
      # Colourize all ATG tags next. One day this may have to become
      # more flexible so that we can colourize codons other than ATG,
      # since e. g. in bacteria, a few genes start with another codon.
      # =================================================================== #
      show_nucleotide_sequence?.display(main_sequence?) { :colourize_start_codon }
      e
      if f? # User supplied an argument in this case
        report_n_start_codons { f? }
      else
        report_n_start_codons
      end
    # ===================================================================== #
    # === orf2?
    # ===================================================================== #
    when /^ORF2\??$/i
      result = search_sequence_for_open_reading_frames(
        :default, :frame2, :default
      )
      erev result
    # ===================================================================== #
    # === fastq_quality_scores
    # ===================================================================== #
    when /^fastq(_|-)?quality(_|-)?scores$/i,
         /^fastq(_|-)?quality(_|-)?schemes$/i,
         /^show(_|-)?fastq(_|-)?quality(_|-)?score(_|-)?table$/i,
         /^fastq(_|-)?table?/
      show_fastq_quality_score_table
    # ===================================================================== #
    # === Visit the human GRCh38.p14 assembly
    # ===================================================================== #
    when /^GRCh38.p14$/i
      open_in_browser 'https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.40'
    # ===================================================================== #
    # === Visit the human GRCh38 assembly
    # ===================================================================== #
    when /^GRCh38$/i
      open_in_browser 'https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/'
    # ===================================================================== #
    # === Feedback which browser is in use
    #
    # Usage example:
    #
    #   browser?
    #
    # ===================================================================== #
    when /^browser\??$/i
      e YAML.load_file(project_yaml_directory?+'configuration/browser.yml')
    # ===================================================================== #
    # === one-to-three
    #
    # This will convert from the one-aminoacid letter to the three-aminoacid
    # letter.
    #
    # Usage example:
    #
    #   1to3 KRKAKAGAGAUUGAUGAAGCCACA # => Lys-Arg-Lys-Ala-Lys-Ala-Gly-Ala-Gly-Ala-Sec-Sec-Gly-Ala-Sec-Gly-Ala-Ala-Gly-Cys-Cys-Ala-Cys-Ala
    #
    # ===================================================================== #
    when /^1to3$/i
      e Bioroebe.one_to_three(a?)
    # ===================================================================== #
    # === set_aminoacids
    # ===================================================================== #
    when 'set_aminoacids',
         'aa_seq',
         'aaseq',
         'setaminoacids',
         'setaa',
         'set_aminoacid',
         'set_aa',
         'setamino',
         'setaminoacid',
         'set_aminoacid_sequence'
      set_aminoacids(a?)
    # ===================================================================== #
    # === stop_codons?
    # ===================================================================== #
    when 'stop_codons?',
         /^stopcodons\??$/,
         'scodons?',
         'look_for_stop_codons_in_the_main_sequence',
         /^report(_|-)?all(_|-)?stop(_|-)?codons$/
      report_all_stop_codons
    # ===================================================================== #
    # === version?
    # ===================================================================== #
    when 'version?',
         'version',
         /^feedback(_|-)?version$/i
      feedback_version
    # ===================================================================== #
    # === CpG?
    # ===================================================================== #
    when /^show(_|-)?cpg(_|-)?islands$/,
         'cg?','CG?','CpG?','CpG',
         'cpg?','cpg','cpg_islands',
         'CPG'
      show_cpg_islands
    # ===================================================================== #
    # === is_on_roebe?
    # ===================================================================== #
    when 'is_on_roebe?'
      erev 'Are we on roebe? '+
           verbose_truth(::Bioroebe.is_on_roebe?.to_s)
    # ===================================================================== #
    # === enable_colours
    # ===================================================================== #
    when 'col',
         'enable_colours',
         'enablecolours',
         'ecolours'
      enable_colours
    # ===================================================================== #
    # === enable_colours_in_an_extended_manner
    # ===================================================================== #
    when /enable(_|-| )?colours(_|-| )?in(_|-| )?an(_|-| )?extended(_|-| )?manner$/
      enable_colours_in_an_extended_manner(:be_verbose)
    # ===================================================================== #
    # === deduce_aa_seq?
    #
    # This entry point will show the possible codons that could code for
    # the given aminoacid at hand.
    #
    # Invocation examples:
    #
    #   deduce_this_aminoacid_sequence AARGLKKKLKLMMAAAAA
    #   deduce MTTAGP
    #   deduce MTTAGKLIIBRRSAAP
    #
    # ===================================================================== #
    when /^deduce(_|-| )?this(_|-| )?aminoacid(_|-| )?sequence$/i,
         'deduce',
         'ded',
         'codons',
         'sof',
         'deduce_aa_seq?',
         'sequence_of',
         'sequenceof',
         'peptide',
         'deduce?',
         /^reverse_?DNA$/i,
         /^revseq$/i
      deduce_this_aminoacid_sequence(f)
    # ===================================================================== #
    # === report_main_sequence
    # ===================================================================== #
    when /^report(_|-)?main(_|-)?sequence$/i,
         'report2'
      report_main_sequence
    # ===================================================================== #
    # === stopcodon?
    # ===================================================================== #
    when /^stop_?codon\??/,
         /^determine_?and_?report_?all_?stop_?codons/
      determine_and_report_all_stop_codons
    # ===================================================================== #
    # === what_sequence_is_this?
    # ===================================================================== #
    when 'what_sequence_is_this?',
         'whatsequenceisthis?',
         'whatsequence'
      what_sequence_is_this?
    # ===================================================================== #
    # === tb1
    #
    # This entry point will start the gtk-controller (some gtk-widgets).
    # ===================================================================== #
    when /^tb1$/i
      remote_URL =
        'https://raw.githubusercontent.com/vsbuffalo/bds-files/master/chapter-03-remedial-unix/tb1-protein.fasta'
      cd log_dir?
      esystem 'wget '+remote_URL
      e 'Downloaded into '+sdir(return_pwd)+'.'
    # ===================================================================== #
    # === add_to_start
    # ===================================================================== #
    when /^add(_|-)?start$/i,
         /^add(_|-)?to(_|-)?start$/i,
         'prepend'
        add_to_start(a?)
    # ===================================================================== #
    # === cd                                                       (cd tag)
    #
    # Usage example:
    #
    #   cd /tmp
    #
    # ===================================================================== #
    when 'cd'
      cd(f)
    # ===================================================================== #
    # === blosum62
    # ===================================================================== #
    when /^-?-?blosum62/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === add_polyA
    # ===================================================================== #
    when 'add_poly_a','add_polyA','polya',
         'addpolya',
         '+polyA',
         'polyA'
      e 'Appending a PolyA sequence to the RNA next (onto @rna).'
      add_poly_a_sequence
    # ===================================================================== #
    # === bioroebe --all_blosum
    # ===================================================================== #
    when /^-?-?all(_|-| )?blosum/i # Show all blosum values here.
      array_all_blosums = %w(
        45 50 62 80 90
      ).map {|entry| entry = entry.dup; entry.prepend('blosum') }
      menu(array_all_blosums)
    # ===================================================================== #
    # === blosum45
    # ===================================================================== #
    when /^-?-?blosum45/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === blosum50
    # ===================================================================== #
    when /^-?-?blosum50/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === gc_content?
    #
    # This entry point will calculate the GC content, as a percentage,
    # of the given input sequence. If no input is given then the
    # default DNA sequence will be used (if assigned).
    #
    # Usage example:
    #
    #   GC? ATGGGGGCGCG
    #
    # ===================================================================== #
    when /^gc_?content\??$/i,
         'calculate',
         'cgc',
         'gcontent',
         'gccc',
         /^GC\??$/i,
         'gccontent?',
         'gc_percent',
         'gcpercent'
      calculcate_gc_content(a?) # This variant will be verbose.
    # ===================================================================== #
    # === www_finder
    #
    # Invocation example:
    #
    #   bioroebe --gtk-www-finder
    #
    # ===================================================================== #
    when 'www_finder',
         'wwwfinder',
         'wfind',
         'wfinder',
         /^-?-?gtk(_|-| )?www(_|-| )?finder$/i
      load_gtk
      require 'bioroebe/gui/gtk3/www_finder/www_finder.rb'
      e 'Starting the WWWFinder next.'
      thread = Thread.new { Bioroebe::GUI::Gtk::WwwFinder.run_gtk3_widget }
      thread.join
    # ===================================================================== #
    # === bioroebe --gtk-levensthein
    # ===================================================================== #
    when /^-?-?gtk(_|-| )?levensthein$/i,
         /^-?-?levensthein(_|-| )?gui$/i
      require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
      Bioroebe::GUI::Gtk::LevenstheinDistance.run
    # ===================================================================== #
    # === count_aminoacids
    # ===================================================================== #
    when 'count_aminoacids',
         'countaminoacids',
         'caminoacids',
         'aminoacid_composition',
         'aminoacidcomposition',
         'acomposition'
      count_amount_of_aminoacids(f)
    # ===================================================================== #
    # === 3iyq.pdb
    # ===================================================================== #
    when '3iyq.pdb'
      download(
        'https://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=fastachain&compression=NO&structureId=3IYR&chainId=B'
      )
    # ===================================================================== #
    # === ubiquitin?
    #
    # This method will simply show the default ubiquitin-sequence.
    # ===================================================================== #
    when 'ubuiquitin?',
         'ubiquitin?',
         'u?',
         'ubiquitin',
         'ub?',
         'return_ubiquitin_sequence',
         'ubi?'
      erev 'N-Terminus '+steelblue(
             ::Bioroebe.return_ubiquitin_sequence
           )+rev+' C-Terminus'
    # ===================================================================== #
    # === KDEL?
    #
    # This entry point will search for a KDEL sequence in the
    # corresponding amino acid sequence.
    #
    # How to test this:
    #
    #   assign AAAAAATTTGGGCCCGCGCCCTTTAAAGATGAACTA; KDEL?
    #
    # ===================================================================== #
    when 'KDEL?',
         'KDEL',
         'find_kdel_sequence'
      find_kdel_sequence
    # ===================================================================== #
    # === bioroebe --blosum80
    # ===================================================================== #
    when /^-?-?blosum80/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === levensthein
    # ===================================================================== #
    when 'levensthein',
         'lst'
      interactive_use_of_levensthein
    # ===================================================================== #
    # === hamming_distance?
    # ===================================================================== #
    when 'hamming','hamming?',
         /^hamming(_|-| )?distance\??$/,
         /^-?-?hamming$/,
         'the_hamming_distance',
         'align'
      calculate_hamming_distance_of(a?)
    # ===================================================================== #
    # === mass_weight?
    # ===================================================================== #
    when 'mass_weight?',
         'mass_weight',
         'massweight',
         'aa_mass',
         'ma' # Calculate weight of proteins.
      mass_weight(f)
    # ===================================================================== #
    # === show_molweight
    #
    # This entry point will show the molecular weights of the four main
    # DNA bases - Adenin, Guanin, Cytosin and Thymin.
    # ===================================================================== #
    when /^show(_|-)?molweight$/i,
         'molweight?',
         'mweight?',
         'm?'
      show_molweight
    # ===================================================================== #
    # === okular
    # === evince
    #
    # This is mostly so that we can quickly use common .pdf viewers.
    # ===================================================================== #
    when 'okular',
         'evince'
      verbose_handle_this_sys_command(i, a?)
    # ===================================================================== #
    # === RNAfold1
    # ===================================================================== #
    when 'RNAfold1'
      esystem 'RNAfold < test.seq'
    # ===================================================================== #
    # === design_polylinker
    # ===================================================================== #
    when /^design(_|-)?polylinker$/i,
         'polylinker?',
         'mcs',
         'mcs?',
         'primer?'
      e colourize_nucleotide(design_polylinker(f))
    # ===================================================================== #
    # === seqsize2
    # ===================================================================== #
    when /seqsize(\d+)/,
         /seq(\d+?)size\??/ # See: http://rubular.com/r/IDvU2LJBSA for the second regex
      _ = $1.to_s.dup
      case _
      when '2'
        report_size_of_this_sequence seq2?,''
      when '3'
        report_size_of_this_sequence seq3?,''
      when '4'
        report_size_of_this_sequence seq4?,''
      when '5'
        report_size_of_this_sequence seq5?,''
      when '6'
        report_size_of_this_sequence seq6?,''
      end
    # ===================================================================== #
    # === set_locus
    # ===================================================================== #
    when /set_?locus/,
         'locus'
      set_locus(a?) # set_locus NM_021964
    # ===================================================================== #
    # === coding_entry
    #
    # This entry point can be used like this:
    #
    #   coding_entry 51..3251
    #
    # ===================================================================== #
    when /^coding_?entry/
      designate_this_input_as_coding_entry(a?)
    # ===================================================================== #
    # === multiline_fasta
    # ===================================================================== #
    when 'multiline_fasta',
         'multilinefasta',
         'mfasta',
         'm_fasta',
         'multi_assign','multiassign','multifasta',/input_?fasta/
      obtain_multiline_fasta # in fasta.rb
    # ===================================================================== #
    # === prosite
    # ===================================================================== #
    when 'prosite',
         'prosite_homepage'
      e 'PROSITE - a database of protein families and domains.'
      e (_ = Bioroebe.try_to_pass_through_beautiful_url(:prosite))
      open_in_browser _
    # ===================================================================== #
    # === restriction_enzymes_run
    # ===================================================================== #
    when 'test_restriction_enzymes_run','restriction_enzymes_run'
      pp restriction_enzymes_run
    # ===================================================================== #
    # === show_jumper_directories
    # ===================================================================== #
    when 'jumper?','jumpers?','show_jumper_directories',
         'showjumperdirectories'
      show_jumper_directories
    # ===================================================================== #
    # === reset
    # ===================================================================== #
    when 'reset',
         'tabula rasa',
         'tabula_rasa',
         'tabula',
         'clear_aa',
         'cleara',
         'clearaa'
      erev 'Resetting the Bioroebe::Shell now.'
      reset_to_the_initial_state
    # ===================================================================== #
    # === set_highlight_colour
    # ===================================================================== #
    when /^set_?highlight_?colour/,'seek'
      _ = f
      _ = _.to_sym if _
      set_highlight_colour_or_search_for_this_sequence(_)
    # ===================================================================== #
    # === to_DNA
    # ===================================================================== #
    when /^to(_|-| )?DNA/i
      e Bioroebe.to_dna('ACCACACCAUUUCCCAUGGGUGUGUGG') # => "ACCACACCATTTCCCATGGGTGTGTGG"
    # ===================================================================== #
    # === files?
    # ===================================================================== #
    when 'files?',
         'file?',
         'files',
         'feedback_where_files_are_kept_locally',
         'feedbackwherefilesarekeptlocally'
      feedback_where_files_are_kept_locally
    # ===================================================================== #
    # === buffer?
    # ===================================================================== #
    when 'buffer?','b?','show_xorg_buffer2',
         'feedback_whether_we_will_also_set_the_xorg_buffer'
      feedback_whether_we_will_also_set_the_xorg_buffer
      show_xorg_buffer
    # ===================================================================== #
    # === toggle
    # ===================================================================== #
    when 'toggle'
      toggle_xorg_buffer
      buffer?
    # ===================================================================== #
    # === average?
    # ===================================================================== #
    when 'average?',
         'average','avg?',
         'show_average',
         'molecular_weight?','mw', # Perhaps we will move the last entry here.
         /show(_|-)?average(_|-)?weight(_|-)?of(_|-)?a(_|-)?nucleotide$/
      show_average_weight_of_an_aminoacid
      show_average_weight_of_a_nucleotide
    # ===================================================================== #
    # === test
    # ===================================================================== #
    when /test/
      e 'THIS IS A TEST.'
    # ===================================================================== #
    # === sigma?
    # ===================================================================== #
    when 'sigma_tutorial',
         'sigma?',
         'sigmatutorial',
         'sig?',
         'stutorial'
      show_sigma_tutorial
    # ===================================================================== #
    # === stop?
    # ===================================================================== #
    when /^stop\??$/i,
         'BLA',
         'end?'
      if dna_sequence?.empty?
        e 'Please first assign a sequence.'
      else
        e
        report_main_sequence(:stop_codon)
        e
      end
    # ===================================================================== #
    # === mode?
    # ===================================================================== #
    when 'mode?',
         /^report(_|-)?mode$/i
      report_mode
    # ===================================================================== #
    # === todo?
    # ===================================================================== #
    when 'todo?'
      _ = 'https://www.biostars.org/'
      show_todo_file
      erev 'Also consider visiting: '
      e
      erev "  #{_}"
      e
      set_xclip _
    # ===================================================================== #
    # === numbered?
    # ===================================================================== #
    when /^numbered\??/,
         /^with(_|-)?numbers$/i,
         /^show(_|-)?numbered(_|-)?nucleotide(_|-)?positions$/i
      show_numbered_nucleotide_positions
    # ===================================================================== #
    # === padding?
    # ===================================================================== #
    when 'padding?'
      pp padding?
    # ===================================================================== #
    # === Handle +3 and similar instructions
    # ===================================================================== #
    when /^\+(\d+)/ # See http://rubular.com/r/JaeO91V1vt
      add_n_nucleotides($1)
    # ===================================================================== #
    # === highlight
    # ===================================================================== #
    when /^highlight/,'high' # ← This variant is always verbose.
      set_highlight_colour(f, :be_verbose)
    # ===================================================================== #
    # === show_all_codon_tables
    # ===================================================================== #
    when 'show_all_codon_tables',
         'all_codon_tables',
         'atables',
         'alltable?',
         'showallcodontables',
         'codons?',
         'codontables',
         'codontables?',
         'show3',
         'showtables',
         'show_codon_tables'
      show_all_codon_tables
    # ===================================================================== #
    # === seq3?
    # ===================================================================== #
    when 'seq3?','s3?'
      show_seq_3
    # ===================================================================== #
    # === seq4?
    # ===================================================================== #
    when 'seq4?','s4?'
      show_seq_4
    # ===================================================================== #
    # === seq5?
    # ===================================================================== #
    when 'seq5?','s5?'
      show_seq_5
    # ===================================================================== #
    # === seq6?
    # ===================================================================== #
    when 'seq6?','s6?'
      show_seq_6
    # ===================================================================== #
    # === do_analyze_protein_sequence
    # ===================================================================== #
    when 'do_analyze_protein_sequence','do_analyze_sequence',
         'doanalyzesequence','analyze_sequence','analyzesequence'
      do_analyze_sequence
    # ===================================================================== #
    # === glycolysis?
    # ===================================================================== #
    when 'glycolysis?',
         'glykolyse?',
         'glykolyse',
         'glycolysis',
         'glykolysis',
         'display_glycolysis_pathway',
         'glyk?',
         'glyc?'
      display_glycolysis_pathway
    # ===================================================================== #
    # === result?
    # ===================================================================== #
    when 'result?'
      e @internal_hash[:result]
    # ===================================================================== #
    # === cysteines?
    #
    # This entry point will quickly show all cysteines in the given
    # aminoacid sequence. This is meant mostly as a visual aid to
    # the user on the commandline.
    # ===================================================================== #
    when /^-?-?cysteines\??$/i
      _ = aminoacid_sequence? # Get our aminoacid sequence first.
      erev _.to_s.gsub(/C/, gold('C')+rev)
    # ===================================================================== #
    # === Handle -3 and similar instructions
    # ===================================================================== #
    when /^\-(\d+)/
      remove_n_nucleotides($1)
    # ===================================================================== #
    # === pad
    # ===================================================================== #
    when 'pad'
      e pad?+f.to_s
    # ===================================================================== #
    # === ori?
    # ===================================================================== #
    when 'ori?',
         'show_ori_sequences',
         'showorisequences'
      show_ori_sequences
    # ===================================================================== #
    # === short_aa
    # ===================================================================== #
    when 'short_aa',
         'shortaa',
         'shorten_aa'
      dna_to_aminoacid_sequence(a?)
    # ===================================================================== #
    # === add_his_tag
    # ===================================================================== #
    when /add(_|-)?his(_|-)?tag/
      add_his_tag('add 6 random his tags') 
    # ===================================================================== #
    # === names? 
    # ===================================================================== #
    when 'names?'
      show_how_to_use_the_names_for_the_taxonomy_table
    # ===================================================================== #
    # === gem?
    # ===================================================================== #
    when 'gem?','rubygem?',
         /^bioroebe(_|-)?gem/
      remote_URL = 'https://rubygems.org/gems/bioroebe'
      e remote_URL
      open_in_browser(remote_URL) if is_on_roebe?
    # ===================================================================== #
    # === set_download_folder
    # ===================================================================== #
    when /^set(_|-)?download(_|-)?folder$/i,
         'set_download_directory',
         'setdownloaddirectory',
         'setdir'
      set_download_directory(f)
    # ===================================================================== #
    # === parse_taxonomy
    # ===================================================================== #
    when /^parse_?taxonomy/,
         'ptaxo',
         'ptax'
      ParseTaxonomy.new(a?)
    # ===================================================================== #
    # === bisulfite
    #
    # Apply a bisulfite-run against the current sequence at hand.
    #
    # Usage examples:
    #
    #   bisulfite CCCGCAATGCATACCTCGCCG
    #   bis CCCGCAATGCATACCTCGCCG
    #
    # ===================================================================== #
    when /^bisulfite$/,
         /^bis$/
      e format_this_nucleotide_sequence(
          bisulfite(a?)
        )
    # ===================================================================== #
    # === longest_substring?
    #
    # Usage example:
    #
    #   longest_substring? ATGGGAAT GGG
    #
    # ===================================================================== #
    when /^longest(_|-)?substring\??$/,
         /^LCS$/i,
         'McIlroy-Hunt algorithm'
      find_longest_substring_via_LCS(a?)
    # ===================================================================== #
    # === yaml_engine?
    # ===================================================================== #
    when /^yaml(_|-)?engine\??$/i,
         /^report(_|-)?which(_|-)?yaml(_|-)?engine(_|-)?is(_|-)?in(_|-)?use$/, # === report_which_yaml_engine_is_in_use
         /^syck\??$/i
      report_which_yaml_engine_is_in_use
    # ===================================================================== #
    # === ecoli
    # ===================================================================== #
    when /ecoli\??/
      erev '  https://ecocyc.org/'
    # ===================================================================== #
    # === selenocysteine
    # ===================================================================== #
    when /selenocysteine\??/
      erev 'UGA codes for selenocysteine.'
    # ===================================================================== #
    # === aa_analyze?
    # ===================================================================== #
    when 'aa_analyze?',
         'aa_analyze',
         'aminoacid_sequence?',
         /aminoacidsequence\??/,
         'aminoacid_analyze',
         'aminoacidanalyze',
         'protein_composition?',
         'asequence',
         'asequence?'
      show_protein_composition(aminoacid_sequence?)
      molecular_mass_of_amino_acids_in_this_sequence(aminoacid_sequence?)
    # ===================================================================== #
    # === find_TATA
    # ===================================================================== #
    when 'tata?','tata','TATA?',
         /^find(_|-)?TATA\??$/
      search_for_tata_consensus_sequence
    # ===================================================================== #
    # === restore_prompt
    # ===================================================================== #
    when /^restore(_|-)?prompt$/i,
         /^restore(_|-)?default(_|-)?prompt$/i
      restore_default_prompt
    # ===================================================================== #
    # === BASE_DIR
    # ===================================================================== #
    when /^BASE(_|-)?DIR$/i
      e sdir(Bioroebe.base_directory?)
    # ===================================================================== #
    # === histone_table?
    # ===================================================================== #
    when 'histone_table?','htable','show_histone_table','showhistonetable'
      show_histone_table
    # ===================================================================== #
    # === primer
    # ===================================================================== #
    when 'primer'
      primer(f)
    # ===================================================================== #
    # === GFF
    # ===================================================================== #
    when /^GFF\??$/i
      show_information_about_the_gff_format
    # ===================================================================== #
    # === frame1
    # ===================================================================== #
    when 'frame1',
         'f1',
         'f'
      showorf(dna_sequence?, :frame1)
    # ===================================================================== #
    # === open_in_browser
    #
    # Usage example:
    #
    #   oib https://www.uniprot.org/uniprot/P62897
    #
    # ===================================================================== #
    when /^open(_|-)?in(_|-)?browser$/i,
         'oib'
      open_in_browser(a?)
    # ===================================================================== #
    # === composition?
    #
    # This entry point will show the composition of the given DNA sequence
    # at hand.
    # ===================================================================== #
    when /^show(_|-)?composition$/,
         'composition?',
         'composition',
         'comp',
         'compo',
         'compo?',
         'comp?',
         'scompo'
      show_composition
    # ===================================================================== #
    # === load
    # ===================================================================== #
    when 'load',
         /^load(_|-)?from$/i,
         /^use$/i
      load(a?)
    # ===================================================================== #
    # === load_dna
    # ===================================================================== #
    when /^load(_|-)?dna$/i
      load_dna
    # ===================================================================== #
    # === transeq
    # ===================================================================== #
    when 'transeq','transseq','teq'
      i = a?
      i = dna_sequence? unless i
      if i.is_a?(Array) and i.empty?
        i = dna_sequence?
      end
      ::Bioroebe::DnaToAminoacidSequence.new(i) { :be_verbose } # bl dna/dna_to_aminoacid_sequence.rb
    # ===================================================================== #
    # === display_open_reading_frames
    #
    # Usage example:
    #
    #   display_open_reading_frames ATGAGCAAGGCCGACTACGAGAAG
    #
    # ===================================================================== #
    when /^display(_|-)?open(_|-)?reading(_|-)?frames$/i
      display_open_reading_frames(a?) { :show_three_frames }
    # ===================================================================== #
    # === ruler-no-colours
    # ===================================================================== #
    when /^-?-?ruler(_|-)?no(_|-)?colours?$/,
         'ruler2'
      show_sequence_with_a_ruler(first_argument?) { :without_colours }
    # ===================================================================== #
    # === reverse
    # ===================================================================== #
    when 'reverse',
         /^reverse(_|-)?sequence$/,
         'reverse_seq' # This will reverse the complement.
      show_reverse_dna_string
    # ===================================================================== #
    # === reverse!
    # ===================================================================== #
    when 'reverse!'
      set_dna_sequence(return_reverse_dna_string)
    # ===================================================================== #
    # === aasize
    # ===================================================================== #
    when 'aasize',
         'asize',
         'aasize?',
         'aa_size?',
         /^report(_|-)?aminoacid(_|-)?size$/i,
         'reportaasize'
      report_how_many_aminoacids_we_have
    # ===================================================================== #
    # === base_composition
    #
    # Use this like so:
    #
    #    base_composition 10 20 30 40
    #    base_composition 5 5 5 85
    #
    # ===================================================================== #
    when /base_composition/
      hash = {}
      hash[:A] = 0
      hash[:T] = 0
      hash[:C] = 0
      hash[:G] = 0
      hash[:A] = a?[0].to_i
      hash[:T] = a?[1].to_i
      hash[:C] = a?[2].to_i
      hash[:G] = a?[3].to_i
      display_this_sequence(
        Bioroebe.generate_random_dna_sequence(
          :default,
          hash
        )
      )
    # ===================================================================== #
    # === shuffle
    # ===================================================================== #
    when 'shuffle',
         'do_shuffle',
         /^shuffle(_|-)?main(_|-)?string$/i
      shuffle_main_string
    # ===================================================================== #
    # === allweights?
    # ===================================================================== #
    when 'allweights?',
         'allweight',
         'all_weight',
         'allweights',
         'gewicht'
      %w( A T C G U ).each {|entry|
        show_weight_of_this_nucleotide(entry)
      }
    # ===================================================================== #
    # === default
    # ===================================================================== #
    when 'default','def','d' # default action to use.
      i = 'shorten Lys Ser Pro Ser Leu Asn Ala Ala Lys'
      check_input_against_case_menu
    # ===================================================================== #
    # === upcase
    # ===================================================================== #
    when 'upcase',
         'ucase',
         'upcase_main_string',
         'upcasemainstring',
         'uppercase',
         'to_upper',
         'upcas'
      upcase_main_string
    # ===================================================================== #
    # === weight_of_common_proteins?
    #
    # This entry point allows us to show the weight of some common
    # problems, e. g. for easy commandline-display.
    # ===================================================================== #
    when /^weight(_|-)?of(_|-)?common(_|-)?proteins\??/,
         /^show(_|-)?the(_|-)?weight(_|-)?of(_|-)?some(_|-)?common(_|-)?proteins/,
         /^protein(_|-)?mass\??/,
         /^table(_|-)?weights$/i,
         /^weight(_|-)?table$/i,
         'molecular_weights?',
         'sizes?',
         'weights',
         'massweights',
         'molweights?',
         'masssize',
         'showweights',
         'proteins?'
      show_the_weight_of_some_common_proteins
    # ===================================================================== #
    # === protein_weight?
    # ===================================================================== #
    when /^protein(_|-)?weight\??/i,
         /^report(_|-)?the(_|-)?protein(_|-)?weight$/i
      report_the_protein_weight
    # ===================================================================== #
    # === show_weight_of_this_nucleotide
    # ===================================================================== #
    when 'show_weight_of_this_nucleotide',
         'molweight',
         'showweightofthisnucleotide'
      show_weight_of_this_nucleotide(f)
    # ===================================================================== #
    # === weights?
    # ===================================================================== #
    when 'weights?'
      MolecularWeightOfNucleotides.report_weight
    # ===================================================================== #
    # === controller
    #
    # This entry point will start the gtk-controller (some gtk-widgets).
    #
    # Invocation example:
    #
    #   bioroebe --gui
    #
    # ===================================================================== #
    when /^-?-?controller$/i,
         /^-?-?gui$/i,
         /^-?-?gtk(_|-| )?notebook$/i,   # === bioroebe --gtk-notebook
         /^-?-?gtk(_|-| )?controller$/i,
         /^-?-?notebook$/i
      start_gtk_controller
      # =================================================================== #
      # === download                                   (download tag, dl tag)
      #
      # Generic download-related entry point. This can be used like in
      # the following way:
      #
      #   download lambda
      #
      # =================================================================== #
      when /^download$/i
        download(a?)
      # =================================================================== #
      # === download?
      # =================================================================== #
      when 'download?',
           'show_last_downloaded_file',
           'showlastdownloadedfile'
        show_last_downloaded_file
      # =================================================================== #
      # === test
      # =================================================================== #
      when 'test' # Throwaway method for testing.
        # @bioroebe.lazy
        set_dna_sequence '
          ATGTCTGGGGACGCTCCCGATCGGCTCCCGTAACTTACACGGTCTACACAAGACGTGTGTGTATGTCGTCGGACCTTTTAGCTATGAGGCTCGAATGAAGCTACCGAGCCATATCTACGCAGCCTTTTATGGGAACATCAGCATATTTCAATCTACCGCCAGGATGTTGATCCCCGGATGTTAAGGGTTAACCAGTATGATGAACATGGAATTGTGAAGTTACTACGGTTCATTCACGGACGACGCCAAGTTACCATTCTTGCTAACTATCGTCCAGGGATTTTGATATGCATCTGCTCACCTCTGTAGCGGCCTCCCGGAGCTGTCACCACAATC
        '
        e sienna(dna_seq?)
        find_all_orfs
      # =================================================================== #
      # === tphages?
      # =================================================================== #
      when 't-phages?',
         'tphages?',
         /^show(_|-)?t(_|-)?phages$/,
         'tphages',
         'tt','phages?'
      show_t_phages
      # =================================================================== #
      # === raw_sequence?
      # =================================================================== #
      when /^-?-?raw(_|-| )?sequence\??$/i,
           /^-?-?raw(_|-| )?conversion\??$/i
        e sfancy(leading_five_prime)+
          colourize_nucleotide_sequence(
            raw_sequence?, :make_no_modifications
          )+
          sfancy(trailing_three_prime)
    # ===================================================================== #
    # === perform_startup_actions
    # ===================================================================== #
    when /^perform(_|-)?startup(_|-)?actions$/,
         /^startup(_|-)?actions$/
      perform_startup_actions
    # ===================================================================== #
    # === to_fasta
    #
    # toasta is an alias to this entry point.
    # ===================================================================== #
    when /^to(_|-)?f?asta$/i
      to_fasta
    # ===================================================================== #
    # === cat
    # ===================================================================== #
    when 'cat',
         'show_the_content_of_this_file'
      cat(f) # Show the content of a file.
    # ===================================================================== #
    # === blosum?
    # ===================================================================== #
    when 'blosum?',
         'blosum',
         'blosu',
         'blos',
         'blo',
         'bl',
         'b',
         'show_blosum_matrix',
         'matrix',
         'losum'
      show_blosum_matrix
    # ===================================================================== #
    # === debug?
    # ===================================================================== #
    when 'debug?'
      feedback_whether_we_are_in_debug_mode
    # ===================================================================== #
    # === protein_stats?
    # ===================================================================== #
    when 'protein_stats?',
         'protein_stats',
         'pstats?',
         'pstats'
      protein_stats
    # ===================================================================== #
    # === digest
    # ===================================================================== #
    when 'digest',
         /^digest(_|-)?at$/i,
         /^cut(_|-)?with$/i,
         /^cut(_|-)?to$/i
      digest(a?)
    # ===================================================================== #
    # === amino_acids_frequency?
    # ===================================================================== #
    when /^amino(_|-)?acids(_|-)?frequency\??$/i,
         /^show(_|-)?the(_|-)?amino(_|-)?acids(_|-)?frequencies$/i,
         'aa_frequency?',
         'aafrequency?'
      show_the_aminoacids_frequencies
    # ===================================================================== #
    # === basedir?
    # ===================================================================== #
    when /basedir\??/,
         'dir?',
         'base_dir?',
         'log_dir',
         'log_dir?'
      show_config_dir
      show_save_file
      show_log_dir
    # ===================================================================== #
    # === show_log_dir
    # ===================================================================== #
    when /^show(_|-)?log(_|-)?dir$/,
         'logdir?',
         'logdir',
         'sdir?',
         'slog',
         'log?',
         /^-?-?location\??$/i,
         'localdir?'
      show_log_dir
    # ===================================================================== #
    # === set_log_dir
    #
    # This entry point can be used to set a specific log directory
    # from within a running instance of the bioshell.
    #
    # Invocation examples:
    #
    #   set_log_dir /tmp/test
    #   setlogdir /tmp/test
    #
    # ===================================================================== #
    when /^set(_|-)?log(_|-)?dir$/i
      set_log_dir(first_argument?) { :be_verbose }
    # ===================================================================== #
    # === chunked_display
    #
    # Usage example:
    #
    #   cdisplay ATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACAC
    #
    # ===================================================================== #
    when /^chunked(_|-)?display$/i,
         'properly_number','cdisplay',
         'chunked',
         'chunk',
         /^beautify(_|-)?body$/
      chunked_display(a?)
    # ===================================================================== #
    # === *
    # ===================================================================== #
    when '*'
      erev 'The occurrence of * in a amino acid sequence denotes a STOP codon.'
    # ===================================================================== #
    # == mmass
    #
    # Usage example:
    #
    #   molmass Glycine
    #
    # ===================================================================== #
    when 'mmasse',
         'molecular_mass_of',
         'molecularmassof',
         'mmase',
         'masse?',
         'molmasse',
         'molmass'
      molecular_mass_of(f)
    # ===================================================================== #
    # === showorf
    # ===================================================================== #
    when /^showorfs?$/,
         'showor',
         'show_orf',
         'show_the_orf'
      showorf(a?)
    # ===================================================================== #
    # === bioshell --permanently-disable-startup-intro
    # ===================================================================== #
    when /^-?-?permanently(_|-)?disable(_|-)?startup(_|-)?intro$/
      permanently_disable_startup_intro
    # ===================================================================== #
    # === startup_info?
    #
    # This entry point exists mostly as a debug-aid.
    # ===================================================================== #
    when /^-?-?startup(_|-)?info\??$/i,
         /^-?-?show(_|-)?startup(_|-)?information$/i,
         /^-?-?show(_|-)?intro$/i,
         /^-?-?sintro$/
      show_startup_information
    # ===================================================================== #
    # === downcase_main_string
    # ===================================================================== #
    when /^downcase(-|_| )?main(-|_| )?string$/,
         /^downcase$/i,
         'dcase',
         'down',
         'lower'
      downcase_main_string
    # ===================================================================== #
    # === silent-startups
    # ===================================================================== #
    when /^-?-?silent(-|_)?startup$/,
         /^-?-?silent$/
      do_a_silent_startup
    # ===================================================================== #
    # === seqsize?
    # ===================================================================== #
    when 'seqsize?'
      e sequence?.to_s.size
    # ===================================================================== #
    # === alu?
    # ===================================================================== #
    when 'alu?',
         'show_alu_sequence',
         'alu_sequence?'
      show_alu_sequence
    # ===================================================================== #
    # === positions?
    # ===================================================================== #
    when 'positions?','positions',
         'show_positions','showpositions',
         'show_position_of_sequence','showpositionofsequence',
         'pos?'
      show_position_of_sequence
    # ===================================================================== #
    # === codon_usage_analyzer
    # ===================================================================== #
    when /^codon_?usage_?analyzer/
      ShowCodonUsage.new(dna_string?)
    # ===================================================================== #
    # === return_all_genes
    # ===================================================================== #
    when 'return_all_genes',
         'returnallgenes'
      return_all_genes
    # ===================================================================== #
    # === install
    # ===================================================================== #
    when 'install'
      install(f)
    # ===================================================================== #
    # === enable
    # ===================================================================== #
    when 'enable',
         'use'
      enable(a?)
    # ===================================================================== #
    # === do_use_expand_cd_aliases
    # ===================================================================== #
    when 'do_use_expand_cd_aliases',
         'douseexpandcdaliases',
         'cdaliases',
         /use(_|-)?expanded(_|-)?aliases$/i # === use_expanded_aliases
      enable :cd_aliases
    # ===================================================================== #
    # === do_not_use_expand_cd_aliases
    # ===================================================================== #
    when 'do_not_use_expand_cd_aliases',
         'no_expand_cd_aliases',
         'no_cd_aliases'
      disable :cd_aliases
    # ===================================================================== #
    # === use_expand_cd_aliases?
    # ===================================================================== #
    when /^use(_|-)?expand(_|-)?cd(_|-)?aliases\??$/i,
         '@use_expand_cd_aliases',
         /^report(_|-)?whether(_|-)?we(_|-)?will(_|-)?make(_|-)?use(_|-)?of(_|-)?expand(_|-)?cd(_|-)?aliases$/i
      report_whether_we_will_make_use_of_expand_cd_aliases
    # ===================================================================== #
    # === pir
    # ===================================================================== #
    when 'pir?',
         'pir'
      e "  #{Bioroebe.try_to_pass_through_beautiful_url('pir').first}"
    # ===================================================================== #
    # === chromosome_table
    # ===================================================================== #
    when /^chromosome(_|-)?table$/i,
         /^show(_|-)?chromosome(_|-)?table$/i
      show_chromosome_table
    # ===================================================================== #
    # === findgene?
    # ===================================================================== #
    when 'findgene?',
         'notify_the_user_as_to_how_findgene_works'
      notify_the_user_as_to_how_findgene_works
    # ===================================================================== #
    # === calculate_exponential_growth
    #
    # Invocation example:
    #
    #   calculate_exponential_growth 1, 10
    #
    # ===================================================================== #
    when /calculate(_|-)?exponential(_|-)?growth$/
      calculate_exponential_growth(first_argument, second_argument)
    # ===================================================================== #
    # === test_help
    # ===================================================================== #
    when 'test_help','testhelp','new_help','newhelp','1'
      ::Bioroebe::Shell::Help[]
    # ===================================================================== #
    # === fasta1
    #
    # This entry point allows us to quickly refer to different
    # FASTA entries from a file, such as:
    #
    #   fasta5 # refers to the 5th entry
    #   fasta6 # refers to the 6th entry
    #   ^^^ and so forth
    #
    # ===================================================================== #
    when /^fasta(\d{1,10})$/i
      try_to_display_this_fasta_entry($1.to_s.dup) { :and_assign_it_as_well }
    # ===================================================================== #
    # === will_we_truncate?
    # ===================================================================== #
    when 'truncate?',
         'will_we_truncate?'
      will_we_truncate?
    # ===================================================================== #
    # === When it starts with one or more numbers, including a ' '.
    #     Example: 100 aa
    # ===================================================================== #
    when /^\d+ aa/ # See: http://rubular.com/r/Lnf2b9RTGP
      case f
      when 'aa'
        create_n_random_amino_acids(_)
      end
    # ===================================================================== #
    # === append_aminoacid
    # ===================================================================== #
    when 'append_aminoacid',
         'add_aa',
         'addaa',
         'append_aa' # Append to aa.
      @internal_hash[:aminoacids] << a
    # ===================================================================== #
    # === find_nls
    # ===================================================================== #
    when 'find_nls',
         'nls',
         'nls_finder',
         'nlsfinder',
         'run_nls_search'
      run_nls_search
    # ===================================================================== #
    # === GFP?
    # ===================================================================== #
    when 'GFP?',
         /^show_?GFP_?sequence$/i,
         /^gfp\??/
      erev "The #{rosybrown('GFP sequence')}#{rev} is:#{N}#{N}"
      show_GFP_sequence
      e
      erev 'Note: If you wish to assign this as the new main nucleotide'
      erev 'sequence, then use this command:'
      e
      erev '  '+sfancy('  assign :GFP')
      e
    # ===================================================================== #
    # === colourize_fasta
    # ===================================================================== #
    when 'colourize_fasta',
         'colourizefasta',
         'colourize_fasta_file',
         'colourizefastafile'
      colourize_fasta_file(a?)
    # ===================================================================== #
    # === urls?
    # ===================================================================== #
    when 'urls?',
         'url?'
      e 'Showing some URLs next:'
      e
      erev '  ftp://ftp.ncbi.nih.gov/genbank/'
      erev '  https://rosalind.info/problems/list-view/'
      erev '  https://biotools.umassmed.edu/bioapps/primer3_www.cgi # Primerdesign'
      e
      pdb_url? # And also show the PDB Url.
    # ===================================================================== #
    # === loxp?
    # ===================================================================== #
    when 'loxp?',
         'loxp'
      erev 'Next showing the loxP sequence:'
      _ = 'ATAACTTCGTATA'
      e
      e sfancy(_)
      e
      find_this_sequence(_) unless dna_sequence?.empty?
    # ===================================================================== #
    # === blast
    # ===================================================================== #
    when 'blast'
      open_blast_webpage
    # ===================================================================== #
    # === telomer?
    # ===================================================================== #
    when 'telomer?',
         'telomere?'
      e padding?+leading_five_prime+'TTAGGG'+trailing_three_prime
    # ===================================================================== #
    # === save_my_file
    # ===================================================================== #
    when /^save(_|-)?my(_|-)?file$/,
         'save'
      save_my_file { :be_verbose }
    # ===================================================================== #
    # === rev?
    # ===================================================================== #
    when 'rev?'
      e 'Testing rev next, the ability to revert to the default colour.'
      pp ::Bioroebe.rev
      if ::Bioroebe.rev.empty?
        e 'Not using any special colours presently.'
      else
        e 'Using special colours.'
      end
      e "Red then revert, if colours are enabled: "\
        "#{swarn('Red then')}#{rev} revert."
    # ===================================================================== #
    # === available_colours?
    # ===================================================================== #
    when /^available_?colours\??/,
         /^show_?html_?colours/,
         'highlight?'
      show_html_colours
    # ===================================================================== #
    # === seq_with_tab?
    # ===================================================================== #
    when /seq_?with_?tab\??/,
         'splitted',
         'splitter'
      show_string { :with_colourized_separator }
    # ===================================================================== #
    # === barrier
    # ===================================================================== #
    when 'barrier','vertical','verti',
         /^add(_|-)?vertical(_|-)?barrier(_|-)?to(_|-)?sequence$/
      add_vertical_barrier_to_sequence(a?)
    # ===================================================================== #
    # === seq5
    # ===================================================================== #
    when /seq5/
      @internal_hash[:array_sequences[4]] = only_valid_dna_nucleotides(a?)
    # ===================================================================== #
    # === pdf_tutorial
    # ===================================================================== #
    when 'generate_pdf_tutorial',
         'generatepdftutorial',
         'generate_pdf_documentation',
         'gpdf',
         'pdf_tutorial',
         'create_pdf'
      erev 'Next creating a .pdf file that includes the Tutorial.'
      generate_pdf_tutorial
    # ===================================================================== #
    # === GenbankFlatFileFormatGenerator
    # ===================================================================== #
    when /^Genbank_?Flat_?File_?Format_?Generator/i
      if File.exist? f
        object = GenbankFlatFileFormatGenerator.new(f)
        pp object
      else
        no_file_exists_at(f)
      end
    # ===================================================================== #
    # === bla
    # ===================================================================== #
    when 'bla' # This is just a test.
      e Bioroebe.store_here?
      e Bioroebe.log_dir
    # ===================================================================== #
    # === debug_seq?
    # ===================================================================== #
    when 'debug_seq?'
      pp string? # Show in a "debug" variant.
    # ===================================================================== #
    # === lernen
    # ===================================================================== #
    when 'lernen'
      _ = 'https://www.biostars.org/'
      e 'Now opening '+_
      open_in_browser(_)
    # ===================================================================== #
    # === peroxisome_pts1
    # ===================================================================== #
    when 'peroxisome_pts1'
      erev '-Ser-Lys-Leu-COOH'
    # ===================================================================== #
    # === atp_cost?
    #
    # Usage example:
    #
    #   atp_cost? 2
    #
    # ===================================================================== #
    when 'atp_cost?',
         'atpcost?',
         'atpcost',
         'atp?'
      calculate_atp_cost_for(a?)
    # ===================================================================== #
    # === vectors?
    # ===================================================================== #
    when /^-?-?vectors\??/,
         /^-?-?show_?available_?vectors?/,
         /^-?-?show_?vector/
      show_available_vectors # show_available_vectors
    # ===================================================================== #
    # === seq3
    # ===================================================================== #
    when /seq3/
      @internal_hash[:array_sequences[2]] = only_valid_dna_nucleotides(a?)
    # ===================================================================== #
    # === seq4
    # ===================================================================== #
    when /seq4/
      @internal_hash[:array_sequences[3]] = only_valid_dna_nucleotides(a?)
    # ===================================================================== #
    # === agarose_table
    # ===================================================================== #
    when /agarose_?table/,
         /show_?agarose_?table/,
         /show_?agarose_?concentration/,
         'agarose'
      show_agarose_table
    # ===================================================================== #
    # === gene_name
    # ===================================================================== #
    when /gene_?name/,
         /set_?name_?of_?gene/,
         'gename',
         'set_name',
         'setname',
         'genename?',
         'setgene',
         'setgen',
         /name_?of_?gene/
      set_name_of_gene(a?)
    # ===================================================================== #
    # === codon_headers
    # ===================================================================== #
    when /codon(_|-)?headers/i,
         'codon_tables_headers',
         'codontablesheaders',
         'headercodon',
         'ctables',
         /^show(_|-)?all(_|-)?codon(_|-)?tables$/i
      show_all_codon_tables(:headers)
    # ===================================================================== #
    # === save?
    # ===================================================================== #
    when 'save?',
         /show_?save_?file/
      show_save_file
    # ===================================================================== #
    # === human_genome_version?
    #
    # Simply show the current human genome version.
    # ===================================================================== #
    when /human(_|-)?genome(_|-)?version\??/,
         /show(_|-)?human(_|-)?genome(_|-)?version$/i
      show_human_genome_version
    # ===================================================================== #
    # === show_aminoacids_residues
    # ===================================================================== #
    when /^show(_|-)?aminoacids(_|-)?residues$/i
      show_aminoacids_residues
    # ===================================================================== #
    # === save_here
    # ===================================================================== #
    when 'save_here',
         'savehere',
         /report(_|-| )?where(_|-| )?we(_|-| )?store$/i
      set_save_file(:default)
      report_where_we_store
    # ===================================================================== #
    # === show_codon_usage
    #
    # This entry point allows the user to analyse the codon usage of
    # the given argument.
    # ===================================================================== #
    when /codon(_|-| )?usage$/i,
         /show(_|-| )?codon(_|-| )?usage$/i,
         'cusage',
         'codo',
         'susage',
         /^-?-?codonusage\??$/i
      show_codon_usage(all_arguments?)
    # ===================================================================== #
    # === quit
    #
    # This entry point will honour all valid ways to exit,
    # store in the constant VALID_WAYS_TO_EXIT.
    # ===================================================================== #
    when *VALID_WAYS_TO_EXIT # bl $BIOROEBE/constants/constants.rb
      do_quit # Quit tag.
    else # else tag
      i = i.first if i.is_a? Array
      return if i.nil?
      # =================================================================== #
      # === First check whether we have a global environment variable.
      #
      # If so then this will be converted.
      # =================================================================== #
      i = convert_global_env(i) if i.to_s.include? '$'
      # =================================================================== #
      # === Handle ExpandCdAliases next
      #
      # Next, check whether we can use the cd-aliases.
      # =================================================================== #
      if use_expand_cd_aliases? and is_this_a_cd_alias?(i)
        target = ::Rcfiles::DirectoryAliases[i]
        cd(target)
      # =================================================================== #
      # === Handle existing local .pdb files next
      #
      # Since as of July 2022 this will also consider downloading
      # a remote .pdb file, if no such file exists yet - not in
      # this clause, but in the very next clause.
      # =================================================================== #
      elsif i and i.end_with?('.pdb') and File.exist?(i)
        parse_pdb_file(i)
      # =================================================================== #
      # === Download missing .pdb files here
      #
      # This must be closely kept in sync with the entry clause above.
      #
      # Usage example:
      #
      #   1hzh.pdb
      #
      # =================================================================== #
      elsif i.end_with?('.pdb') and !File.exist?(i.downcase)
        i = i.downcase
        unless File.exist?(::Bioroebe.pdb_directory?+File.basename(i))
          _result = download_this_pdb_file(i)
        else
          e 'The file already exists at `'+
             sfile(::Bioroebe.pdb_directory?+File.basename(i))+'`.'
        end
      # =================================================================== #
      # === Handle sequence assignments
      #
      # This entry clause is entered if the input consists of only valid
      # DNA nucleotides. Since as of December 2021 we will ignore
      # newlines that are part of the input sequence.
      #
      # Example to enter this clause:
      #
      #   ATGAGCAAGGCCGACTACGAGAAG
      #
      # =================================================================== #
      elsif only_valid_dna_nucleotides?(i.delete('-'))
        set_dna_sequence(i.delete('-'), :be_verbose) { :show_the_sequence_as_well }
      # =================================================================== #
      # === Handle downcased sequence assignments as well
      # =================================================================== #
      elsif only_valid_dna_nucleotides?(i.upcase.delete('-'))
        set_dna_sequence(i.upcase.delete('-'), :be_verbose)
      # =================================================================== #
      # === Handle input such as "227 / 3"
      # =================================================================== #
      elsif i.include?('/') and (i =~ /\d+/)
        result = eval(i)
        e result
      # =================================================================== #
      # === Intercept 3' input given to us.
      # =================================================================== #
      elsif original_input.to_s.strip.start_with?("3'-") # 3'-ATGCCTGCC
        find_complementary_strand(original_input)
      # =================================================================== #
      # === Handle WWW entries by opening them in the browser     (www tag)
      #
      # This includes "https" evidently as well.
      # =================================================================== #
      elsif i.start_with?('http')
        open_in_browser(i)
      # =================================================================== #
      # === Check for Aminoacids
      #
      # Check whether the input could be an Aminoacid such as Glycine.
      # =================================================================== #
      elsif could_this_be_an_amino_acid?(i)
        report_everything_about_this_amino_acid(i)
      # =================================================================== #
      # === Check for numbers as input only
      # =================================================================== #
      elsif (i =~ /^\d+$/) and (not main_sequence?.empty?)
        # ================================================================= #
        # Ok, the user did input only numbers. Display these numbers,
        # assumed to refer to the main sequence.
        # ================================================================= #
        _ = main_sequence?
        end_point = i.to_s.to_i - 1
        _ = _[0, end_point] # Must deduct one because we start nucleotide counting at nucleotide 1.
        erev properly_padded_dna_string(_)
      # =================================================================== #
      # === Handle remote fasta files and so forth
      # =================================================================== #
      elsif i.start_with?('http') and
          ( i.end_with?('.fasta') or i.end_with?('.fa') )
        erev 'We have encountered a remote file (fasta). We '\
             'will download it now.'
        this_file = download(i) # Also return this file.
        parse_fasta_format(this_file)
      # =================================================================== #
      # === Handle input starting with @
      # =================================================================== #
      elsif i.start_with? '@'
        e self.instance_variable_get(i)
      # =================================================================== #
      # === Handle nucleotide sequences next
      # =================================================================== #
      elsif is_all_upcase?(i) and only_valid_nucleotides?(i) and !i.empty?
        assign_dna_sequence(i, :be_verbose)
      # =================================================================== #
      # === Handle NCBI links next
      # =================================================================== #
      elsif i.start_with?('http://www.ncbi.') or
            i.start_with?('https://www.ncbi.')
        erev 'Identified a NCBI link. Will assume that this is a '\
             'fasta sequence'
        erev 'and delegate into the method called download_fasta().'
        download_fasta(i)
      # =================================================================== #
      # === Handle fasta input here if the file exists locally (files)
      #
      # This subsection will test for input that is about locally
      # existing files.
      # =================================================================== #
      elsif File.exist?(i) and !File.directory?(i)
        extname = File.extname(i).delete('.')
        case extname
        # ================================================================= #
        # === ps
        # ================================================================= #
        when 'ps' # check for .ps file type
          esystem "gv #{i}"
        # ================================================================= #
        # === fasta
        # ================================================================= #
        when 'fasta','fa'
          parse_fasta_format(i)
        else
          string_to_run = i.to_s+' '+f.to_s
          esystem(string_to_run)
        end
      # =================================================================== #
      # === Handle restriction enzymes
      # =================================================================== #
      elsif i.end_with?('?') or i.include?('Restriction') # if last character is a '?' character.
        @internal_hash[:result] = try_to_find_this_restriction_enzyme(i)
      # =================================================================== #
      # === Handle codons
      # =================================================================== #
      elsif (i.size == 3) and is_this_a_valid_codon?(i)
        e Bioroebe.dna_to_aminoacid_sequence(i)
      # =================================================================== #
      # === Next handle matches against the full line
      #
      # The input is: cytochrome c
      #
      # =================================================================== #
      elsif (original_input =~ /^-?-?cytochrome(_|-| )?c$/i)
        path = download(:cytochrome_c_protein_sequence)
        if File.exist? path
          parse_this_fasta_sequence(path)
        end
      else
        # ================================================================= #
        # === Check whether a local file exists like that
        #
        # The following code will check whether a file exists with the
        # same name in the log-directory. If so then it will be assigned
        # as input-name. Since this may be problematic, we put it into
        # the "else" clause.
        # ================================================================= #
        unless File.exist? i
          if File.exist?(::Bioroebe.log_dir?+i) and 
             File.file?(::Bioroebe.log_dir?+i) # ← Ensure that it really is a file.
            handle_this_file(::Bioroebe.log_dir?+i)
          end
        end
        # =================================================================== #
        # === Handle the case when we did not find the command
        #
        # This here is the final step - if we could not find anything
        # to do with the given input, we will report this to the user.
        # After all, perhaps he made a typo.
        # =================================================================== #
        if report_if_we_did_not_find_the_command # ← FINAL CHECK HERE
          # ================================================================= #
          # Handle .fasta or .fa files in a special way.
          # ================================================================= #
          unless i.empty?
            if i.end_with?('.fasta','fa') and !File.exist?(i)
              # ============================================================= #
              # In this case, try to also find a file with that name in the
              # log-directory of BioRoebe. That way, a user can just
              # copy/paste any URL or local path, and BioRoebe will try to
              # find a file that matches to this input.
              # ============================================================= #
              possible_location = log_dir?+File.basename(i)
              if File.exist? possible_location
                erev 'The given input was not found. However had, the '\
                     'same file was found at:'
                e "  #{sfancy(possible_location)}"
                erev 'This file will be used next.'
                handle_this_fasta_file(possible_location)
                return
              end
            end
            report_this_input_was_not_found(original_input)
          end
        end
      end
    end
  end
end

#mirror_repeat(i = dna_sequence? ) ⇒ Object

#

mirror_repeat

#


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# File 'lib/bioroebe/shell/shell.rb', line 6732

def mirror_repeat(
    i = dna_sequence?
  )
  i = dna_sequence? if i.nil? # Use a proper default in this case.
  i = i.join(' ').strip if i.is_a? Array
  erev default_padding+
       five_prime+
       colourize_dna_sequence(
         ::Bioroebe.mirror_repeat_of(i, :use_separator_token)
       )+
       rev+
       three_trailer
end

#mode? ⇒ Boolean

#

mode?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 10860

def mode?
  @internal_hash[:mode]
end

#molecular_mass_of(i = aminoacids?, , optional_round_here = nil) ⇒ Object

#

molecular_mass_of

Give out the molecular mass of an amino-acid.

We will use only the first input character, and upcase it.

You can also input an Array here, though.

Usage examples:

mmasse tyrosin
mmasse KKKRAAA
mmasse Glycine
#


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# File 'lib/bioroebe/shell/shell.rb', line 6465

def molecular_mass_of(
    i                   = aminoacids?,
    optional_round_here = nil
  )
  case i
  # ======================================================================= #
  # === HELP
  # ======================================================================= #
  when /^-?-?help$/i
    erev 'Input an amino acid, such as H.'
    return
  end if i.is_a? String
  i = aminoacids? if i.nil? # Safeguard.
  # ======================================================================= #
  # === Handle Arrays first
  # ======================================================================= #
  if i.is_a? Array
    i.uniq.each {|entry|
      molecular_mass_of(entry, optional_round_here)
    }
  elsif is_a_registered_compound?(i)
    original_name = i.dup
    # ===================================================================== #
    # This menu is a bit ad-hoc. In the long run we will probably have
    # to make this more generic.
    # ===================================================================== #
    case i
    # ===================================================================== #
    # === Glycine
    # ===================================================================== #
    when /^Glycine?$/i
      i = 'C8H9NO3'
    end
    i = ChemistryParadise.molmass_of?(i)
    erev 'The molecular mass of '+sfancy(original_name)+rev+
         ' is: '+simp(i.to_s.rjust(5))
  else # Else we assume a String here.
    # ===================================================================== #
    # Some input may be like "tyrosin". In this case, we will assume
    # that the user may have input 
    # ===================================================================== #
    if i.size > 1
      if i.size > 3
        _ = i.to_s.downcase
        if _.size > 3
          reversed = AMINO_ACIDS_ABBREVIATIONS.invert
          if reversed.has_key? _
            _ = reversed[_]
            if AMINO_ACIDS_THREE_TO_ONE.has_key? _
              _ = AMINO_ACIDS_THREE_TO_ONE[_]
            end
            molecular_mass_of(_, optional_round_here)
            return
          end
        end
      end
      # =================================================================== #
      # Here, either we grab the mass of each character, or we
      # try to find a single AA replacement.
      # =================================================================== #
      molecular_mass_of(i.chars, optional_round_here)
    else
      if AMINO_ACIDS_MASS_TABLE.has_key? i
        left = rev+'The molecular mass of '+sfancy(i)+rev+' ('+
               get_long_name_of_amino_acid(i)+rev+')'+rev+' is: '
        ljust_value = 72
        ljust_value = 92 if use_colours?
        left = left.ljust(ljust_value)
        result = AMINO_ACIDS_MASS_TABLE[i]
        if optional_round_here
          result = result.to_f.round(optional_round_here)
        end
        erev left+simp(result.to_s.rjust(5))
      else
        # e 'Please input a specific amino acid, such as "H".'
      end
    end
  end
end

#molecular_mass_of_amino_acids_in_the_sequence(i = aminoacid_sequence? ) ⇒ Object Also known as: molecular_mass_of_amino_acids_in_this_sequence

#

molecular_mass_of_amino_acids_in_the_sequence

This method will calculate the mass of all amino acids in the given sequence.

The default input sequence will be the aminoacid sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8540

def molecular_mass_of_amino_acids_in_the_sequence(
    i = aminoacid_sequence?
  )
  total_mass = 0
  if i.is_a? Array # We require a String here really.
    if i.empty? # In this case, assign a default.
      i = aminoacid_sequence?
    else
      i = i.join
    end
  elsif i.nil?
    i = aminoacid_sequence?
  end
  # ======================================================================= #
  # The user may have inputted something such as 'lysine'. In this
  # case, we will convert this to the one-letter code.
  # ======================================================================= #
  if (i != ::Bioroebe.return_short_aminoacid_letter_from_long_aminoacid_name(i))
    i = ::Bioroebe.return_short_aminoacid_letter_from_long_aminoacid_name(i)
  end
  _ = i # Use a copy.
  unless _
    erev 'Please assign an aminoacid sequence.'
    return
  end
  dataset_molecular_formula = YAML.load_file(FILE_AMINOACIDS_MOLECULAR_FORMULA)
  chars =_.chars
  chars.each {|this_aminoacid|
    # ===================================================================== #
    # The following constant has the mass of the aminoacid at hand. It
    # is stored in the one-letter abbreviation.
    # ===================================================================== #
    value = AMINO_ACIDS_MASS_TABLE[this_aminoacid]
    total_mass += value.to_f
    molecular_formula = dataset_molecular_formula[one_letter_to_long_name(this_aminoacid).capitalize]
    erev 'The molecular formula for '+sfancy(this_aminoacid)+rev+
         ' is: '+lightgreen(molecular_formula)+rev
  }
  erev "The total mass (#{seagreen('molecular weight')}#{rev}) of "\
       "this sequence (#{_.size.to_s} entries), using "\
       "#{teal('mono-isotopic mass')}#{rev}, is: "
  if has_konsole?
    erev '  '+cadetblue(total_mass.to_s)
  else
    e "  #{simp(total_mass.to_s)}"
  end
  # ======================================================================= #
  # Next calculate the average mass.
  # ======================================================================= #
  total_mass = 0
  i.chars.each {|this_aminoacid|
    value = AMINO_ACIDS_AVERAGE_MASS_TABLE[this_aminoacid]
    total_mass += value.to_f
  }
  erev "The total mass (#{seagreen('molecular weight')}#{rev}) of "\
       "this sequence (#{_.size.to_s} entries), using "\
       "#{teal('average molecular mass')}#{rev}, is: "
  erev '  '+cadetblue(total_mass.to_s)
end

#move_file_to_its_correct_location(i) ⇒ Object

#

move_file_to_its_correct_location

#


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# File 'lib/bioroebe/shell/shell.rb', line 5730

def move_file_to_its_correct_location(i)
  ::Bioroebe::MoveFileToItsCorrectLocation.new(i)
end

#mutate_aminoacid_position(this_position = 1) ⇒ Object

#

mutate_aminoacid_position

This method will allow us to mutate the aminoacid sequence.

Full usage example:

random 24; show_aminoacid_sequence; mutate_aminoacid_position 1
#


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# File 'lib/bioroebe/shell/shell.rb', line 10977

def mutate_aminoacid_position(this_position = 1)
  if this_position.is_a? Array
    this_position = this_position.join.strip
  end
  this_position = this_position.to_i
  sequence = aa_sequence?
  new_aminoacid = return_random_aminoacid
  old_aminoacid = sequence[this_position-1, 1]
  erev 'We will mutate the aminoacid sequence at position '+
        simp(this_position.to_s)+rev+'. The old aminoacid '
  erev 'was '+simp(old_aminoacid)+rev+', the new aminoacid will '\
       'be '+simp(new_aminoacid)+rev+'.'
  sequence[this_position-1, 1] = new_aminoacid
  show_aminoacid_sequence
end

#mutate_dna_sequence(n_times = 1, old_sequence = dna_sequence? ) ⇒ Object

#

mutate_dna_sequence

Use this method to mutate a DNA nucleotide.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3752

def mutate_dna_sequence(
    n_times      = 1,
    old_sequence = dna_sequence?
  )
  if n_times.is_a? Array
    n_times = n_times.join(' ').strip.to_i
  end
  n_times = n_times.to_i
  n_times.times {
    this_nucleotide_position = rand(old_sequence.size)+1
    do_mutate_dna_sequence_at_this_nucleotide_position(
      this_nucleotide_position, old_sequence
    )
    show_dna_sequence
  }
end

#mutate_position(nucleotide_position, mutate_to_this_nucleotide = return_random_nucleotide) ⇒ Object

#

mutate_position

This method can be used to mutate DNA at a specific position.

Usage example:

random 50; mutate_position 5 C
random 15; mutate_position 1
#


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# File 'lib/bioroebe/shell/shell.rb', line 2106

def mutate_position(
    nucleotide_position,
    mutate_to_this_nucleotide = return_random_nucleotide # Return randomly A, T, C or G here.
  )
  if nucleotide_position.is_a?(String) and nucleotide_position.strip.include?(' ')
    nucleotide_position = nucleotide_position.split(' ')
  end
  # ======================================================================= #
  # === Handle Arrays as input next
  # ======================================================================= #
  if nucleotide_position.is_a? Array # Assume that the user wanted to use things differently then.
    mutate_to_this_nucleotide = nucleotide_position[1]
    nucleotide_position       = nucleotide_position[0]
  end
  old_sequence = dna_sequence?
  do_mutate_dna_sequence_at_this_nucleotide_position(
    nucleotide_position,
    old_sequence,
    mutate_to_this_nucleotide
  )
  show_dna_sequence
end

#n_uracil? ⇒ Boolean

#

n_uracil?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 9694

def n_uracil?
  erev sequence_object?.n_uracil?
end

#name_of_gene? ⇒ Boolean

#

name_of_gene?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6411

def name_of_gene?
  sequence_object?.name_of_gene?
end

#ncbi_nucleotide_search_for(i = '') ⇒ Object

#

ncbi_nucleotide_search_for

#


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# File 'lib/bioroebe/shell/shell.rb', line 7923

def ncbi_nucleotide_search_for(
    i = ''
  )
  i = '' if i.nil? # Reset to default then, in this case.
  i = i.join('+') if i.is_a? Array
  i.strip!
  _ = 'https://www.ncbi.nlm.nih.gov/'.dup
  _ << 'nucgss?term="'+i+'"' unless i.empty? # Use "" quotes to escape shell-code.
  erev 'Now opening '+simp(_)+rev
  open_in_browser _
end

#no_newlines(this_file) ⇒ Object

#

no_newlines

This will get rid of the newlines in a fasta file, at the least for displaying purposes.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9277

def no_newlines(this_file)
  if this_file.is_a? Array
    this_file.each {|entry| no_newlines(entry) }
  else
    dataset = File.readlines(this_file)
    dataset.map! {|line|
      line.chomp! unless line.start_with? '>'
      line
    }
    e dataset.join
  end
end

#notify_the_user_as_to_how_findgene_works ⇒ Object

#

notify_the_user_as_to_how_findgene_works

#


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# File 'lib/bioroebe/shell/shell.rb', line 11170

def notify_the_user_as_to_how_findgene_works
  begin
    _ = project_base_dir?+'find_gene.rb'
    ClassDocuShower[_]
  rescue LoadError
    erev 'Please install class_docu_shower for this functionality to work.'
  end
end

#nucleotide_sequence? ⇒ Boolean Also known as: dna_sequence?, dna_string?, dna_seq?, string?, main_string?, seq?, sequence_1, seq1, seq1?

#

nucleotide_sequence? (string? tag)

Return the DNA sequence in question.

Several aliases exist to this method. It is recommended to use the more explicit name, since this will more accurately reflect the name (and intent) of this method.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 862

def nucleotide_sequence?
  # @internal_hash[:nucleotide_sequence]
  @internal_hash[:array_dna_sequences].last
end

#nucleotides_or_aminoacids? ⇒ Boolean

#

nucleotides_or_aminoacids?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 2532

def nucleotides_or_aminoacids?
  case mode?
  # ======================================================================= #
  # === :dna
  # ======================================================================= #
  when :dna,
       :rna
    'nucleotides'
  # ======================================================================= #
  # === :aminoacids
  # ======================================================================= #
  when :aminoacids
    'aminoacids'
  end
end

#obtain_current_prompt ⇒ Object

#

obtain_current_prompt

This is essentially a getter-method over the instance variable called @internal_hash.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5118

def obtain_current_prompt
  if @internal_hash[:use_working_directory_as_prompt]
    @internal_hash[:prompt_to_use] = return_pwd
  end
  @internal_hash[:prompt_to_use]
end

#obtain_current_prompt_while_honouring_colours ⇒ Object

#

obtain_current_prompt_while_honouring_colours

#


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# File 'lib/bioroebe/shell/shell.rb', line 2473

def obtain_current_prompt_while_honouring_colours
  _ = obtain_current_prompt
  if _ and use_colours?
    _ = "#{Colours::TEAL}#{_}#{rev}"
  end
  return _
end

#obtain_multiline_fasta ⇒ Object

#

obtain_multiline_fasta

If we want to obtain multiline FASTA input, that is input that includes the “n” newline character, then we can use the following method here.

We will use $stdin to obtain the input. The end-delimiter will be _

#


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# File 'lib/bioroebe/shell/shell.rb', line 4466

def obtain_multiline_fasta
  delimiter = ::Bioroebe.delimiter?
  erev 'Input your Fasta format or nucleotide sequence next - '\
       'delimit/end via "'+lightgreen(delimiter)+rev+'" (3x the _ '\
       'character).'
  # ======================================================================= #
  # Chop away all newlines.
  # ======================================================================= #
  dataset = $stdin.gets(delimiter)
  # ======================================================================= #
  # Format the dataset a little.
  # ======================================================================= #
  dataset.chomp!
  dataset.delete!('_')
  dataset.delete!(N)
  dataset.strip!
  parse_fasta_format(dataset)
  # assign_sequence(dataset)
end

#obtain_url_for(i) ⇒ Object

#

obtain_url_for

#


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# File 'lib/bioroebe/shell/shell.rb', line 8716

def obtain_url_for(i)
  ::Bioroebe.try_to_pass_through_beautiful_url(i)
end

#obtain_user_input ⇒ Object Also known as: get_user_input, read_user_input

#

obtain_user_input (input tag)

This method should be used to fetch/read user input. The user input will be kept in an instance variable (called @internal_hash, where @internal_hash is, unsurprisingly, a Hash).

#


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# File 'lib/bioroebe/shell/shell.rb', line 11769

def obtain_user_input
  if readline_is_available?
    # ===================================================================== #
    # This clause is the case for the Readline module.
    # ===================================================================== #
    _ = Readline.readline(
      # =================================================================== #
      # The second argument enables or disables history support.
      # =================================================================== #
      obtain_current_prompt_while_honouring_colours.to_s, true
    )
    # ===================================================================== #
    # === Disallow empty lines to taint the Readline-History
    #
    # Ignore empty lines - or rather, remove them after they were input.
    # ===================================================================== #
    if _ =~ /^\s*$/
      Readline::HISTORY.pop
    # ===================================================================== #
    # If we did input the same command as before, on the previous
    # run, then we will not record this into the readline-history
    # session.
    # ===================================================================== #
    elsif last_inputted_command? == _
      Readline::HISTORY.pop
    end
  else
    # ===================================================================== #
    # This entry point reads in user-input without depending on Readline.
    # ===================================================================== #
    print obtain_current_prompt_while_honouring_colours
    _ = $stdin.gets.chomp
  end
  _.strip! # We do not need or want trailing or leading whitespace.
  unless _.strip.empty? # Ignore empty input given.
    # ===================================================================== #
    # First, let's get rid of input including '#' - these are assumed
    # to be comments and are simply ignored. So, for instance, the
    # input "foo # bar" would be truncated towards "foo" exactly.
    # ===================================================================== #
    if _.include?('#') and (_.size > 1)
      _ = _[0 .. (_.index('#')-1)]
      _.rstrip!
    end
    # ===================================================================== #
    # Next sanitize the situation where the user input consists of only
    # nucleotides, such as ATCG and so forth.
    # ===================================================================== #
    if _.include?(' ') and only_nucleotides?(_.delete(' '))
      _.delete!(' ') # We chop off ' ' tokens, if we only input a nucleotide sequence.
    end
    # ===================================================================== #
    # === Enable multiline input separated via ; next
    # ===================================================================== #
    if _.include? ';'
      _ = _.split(';')
    end
    set_user_input(_)
  end
  return _ # Not strictly necessary, but we return anyway.
end

#only_nucleotides?(i) ⇒ Boolean

#

only_nucleotides?

Just a wrapper over the corresponding module-method.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 5198

def only_nucleotides?(i)
  ::Bioroebe.only_nucleotides?(i)
end

#only_valid_nucleotides?(i) ⇒ Boolean Also known as: only_valid_dna_nucleotides?

#

only_valid_nucleotides?

This method will determine whether our input string (the argument in question) contains only valid nucleotides or whether it does not.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6863

def only_valid_nucleotides?(i)
  i = i.first if i.is_a? Array
  if i.is_a? String
    i = i.delete("\n ").chars
  end
  uniq = i.uniq
  if uniq.all? {|entry| POSSIBLE_DNA_NUCLEOTIDES.include? entry }
    return true
  else
    return false
  end
end

#open_1igt_in_the_browser ⇒ Object

#

open_1igt_in_the_browser

#


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# File 'lib/bioroebe/shell/shell.rb', line 4287

def open_1igt_in_the_browser
  _ = 'https://www.rcsb.org/structure/1igt'
  e; e _; e
  open_in_browser _
end

#open_blast_webpage ⇒ Object

open_blast_webpage

#


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# File 'lib/bioroebe/shell/shell.rb', line 2524

def open_blast_webpage
  open_in_browser_tab 'https://blast.ncbi.nlm.nih.gov/'\
                      'Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome'
end

#open_expasy(i = all_arguments?) ) ⇒ Object

#

open_expasy

#


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# File 'lib/bioroebe/shell/shell.rb', line 6295

def open_expasy(i = all_arguments?)
  _ = 'https://www.expasy.org/'
  open_in_browser(_)
end

#open_in_uniprot(i = 'A1XPA3') ⇒ Object

#

open_in_uniprot

This method will open the remote, associated URL with the protein at hand.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9778

def open_in_uniprot(
    i = 'A1XPA3'
  )
  i = 'A1XPA3' if i.nil? # <- Ensure a default.
  _ = 'https://www.uniprot.org/uniprot/?query='+i+'&sort=score'
  erev _
  set_xclip(_) if configuration?.additionally_set_xorg_buffer
  open_in_browser(_)
end

#open_my_files ⇒ Object

#

open_my_files (open tag, files tag)

This opens some bioroebe-related files.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3822

def open_my_files
  array_my_files = []
  array_my_files << BIOROEBE_AT_HOME+'shell/bioshell.rb'
  array_my_files << BIOROEBE_AT_HOME+'shell/help.rb'
  array_my_files << BIOROEBE_AT_HOME+'shell/menu.rb'
  array_my_files << BIOROEBE_AT_HOME+'bioroebe.rb'
  array_my_files << BIOROEBE_AT_HOME+'constants/constants.rb'
  array_my_files << RUBY_SRC+'/bioroebe/doc/todo/todo.md'
  # array_my_files << BIOROEBE+'/count_amount_of_nucleotides.rb'
  array_my_files.each {|file| open_this_file_in_editor(file) }
end

#open_this_file_in_editor(file) ⇒ Object

#

open_this_file_in_editor (editor tag)

#


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# File 'lib/bioroebe/shell/shell.rb', line 5052

def open_this_file_in_editor(file)
  case file
  when :bioshell, :shell
    file = HOME_DIR+'shell.rb'
  end
  _ = MAIN_EDITOR+' '+file
  if File.exist? file
    splitted = _.split(' ')
    splitted[1][0,0] = sfile
    erev splitted.join(' ')+main_colour
    system _
  else
    erev 'The file `'+sfile(file)+rev+'` does not exist.'
  end
end

#open_this_ncbi_page(i) ⇒ Object

#

open_this_ncbi_page

This method will help us open the proper NCBI pages.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6550

def open_this_ncbi_page(i)
  search_term = i
  search_term = '' if search_term.nil?
  search_term = search_term.join(' ').strip.to_s if search_term.is_a? Array
  if search_term =~ /^\d+$/ # If only numbers.
    _ = '"https://www.ncbi.nlm.nih.gov/gene/'+search_term.to_s+'"'
  else
    _ = '"https://www.ncbi.nlm.nih.gov/gquery/?term='+search_term+'"'
  end
  erev _
  open_in_browser_tab(_)
end

#original_input? ⇒ Boolean Also known as: original_input

#

original_input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 11534

def original_input?
  @internal_hash[:original_input]
end

#padding? ⇒ Boolean Also known as: pad, pad?, lpad?, left_pad?, left_padding?, default_padding

#

padding? (padding tag)

The alias lpad? used to be ‘ ’, but is now simply an alias to this method.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 3960

def padding?
  @internal_hash[:padding]
end

#parse(i) ⇒ Object

#

parse (parse tag)

#


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# File 'lib/bioroebe/shell/shell.rb', line 8013

def parse(i)
  if i.is_a? Array
    i = i.join(' ').strip
  end
  i = i.dup if i.frozen?
  i.chop! if i.end_with?('.')
  # ======================================================================= #
  # We will parse here based on the file-suffix.
  # ======================================================================= #
  case i
  # ======================================================================= #
  # === fasta file
  # ======================================================================= #
  when /\.fasta$/i,
       /\.fa$/i
    parse_fasta_format(i)
    unless array_fasta?.empty?
      # =================================================================== #
      # Assign this dataset next to become the new main sequence.
      # =================================================================== #
      opnerev "We will now assign this data to #{sfancy('@_')}#{rev}."
      set_mode :protein if array_fasta?.last.is_protein?
      assign(array_fasta?.last.sequence)
    end
  # ======================================================================= #
  # === pdb file
  # ======================================================================= #
  when /\.pdb$/i
    parse_this_pdb_file(i)
  else
    erev "Not yet handled: #{steelblue(i)}"
  end
end

#parse_fasta_format(i = nil) ⇒ Object Also known as: parse_this_fasta_file

#

parse_fasta_format

Parse FASTA format here. We will delegate into class Bioroebe::ParseFasta for that.

Usage example:

pfasta NM_001180897.3_Saccharomyces_cerevisiae_S288c_Aga2p_AGA2.fasta
#


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# File 'lib/bioroebe/shell/shell.rb', line 4383

def parse_fasta_format(
    i = nil
  )
  if i.is_a? Array
    i.each {|entry|
      parse_fasta_format(entry)
    }
  else
    # ===================================================================== #
    # === If input is only numbers.
    # ===================================================================== #
    i = Dir['*'][i.to_i + 1] if i =~ /^\d+$/ # <- Only numbers.
    case i
    # ===================================================================== #
    # === ASSIGN
    #
    # This entry point can be used by the user to input ad-hoc data
    # for a FASTA sequence.
    # ===================================================================== #
    when /^ASSIGN$/i
      opnerev 'Input your FASTA Data now (Use __ to terminate input):'
      i = $stdin.gets('__').chomp
    end
    # ===================================================================== #
    # If we did not provide an input, we scan for entries with .fa
    # in the current directory.
    # ===================================================================== #
    if i.nil?
      unless Dir['*.fa'].empty?
        i = Dir['*.fa']
      end
    end
    if i.is_a? Array
      i = i.first
    end
    if i
      erev "Now loading from `#{sfancy(i)}#{rev}`."
    end
    @internal_hash[:fasta_file] = i
    parse_fasta_object = ::Bioroebe.parse_fasta(i) # bl $RSRC/bioroebe/lib/bioroebe/fasta/parse_fasta.rb
    # ===================================================================== #
    # === We will store all created fasta objects in an Array
    # ===================================================================== #
    array_fasta? << parse_fasta_object
    this_sequence = parse_fasta_object.sequence?
    # ===================================================================== #
    # Handle large sequences next - we will add a timer. The purpose of
    # this timer is to notify the user how long it took to assign to
    # the main string. At a later point, we can optimize the speed and
    # do the assignment in pure C rather than ruby.
    # ===================================================================== #
    if this_sequence.size > 1_000_000
      add_timer_snapshot
      erev 'The sequence is fairly large - we will time how long it takes to'
      erev 'assign it to the main sequence.'
    end
    # ===================================================================== #
    # Obtain the type next:
    # ===================================================================== #
    type = parse_fasta_object.type?
    unless type == :protein
      set_dna_sequence(this_sequence)
      if this_sequence.size > 1_000_000
        add_timer_snapshot
        n_seconds_difference = calculate_time_difference.abs.to_f.round(3).to_s
        erev "Loading these #{springgreen(this_sequence.size.to_s)}"\
             "#{rev}"\
             " nucleotides "\
             "took #{sfancy(n_seconds_difference)}#{rev} seconds."
      end
    end
  end
end

#parse_this_fasta_sequence(i) ⇒ Object

#

parse_this_fasta_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 3650

def parse_this_fasta_sequence(i)
  if i and File.file?(i)
    set_aminoacid(File.read(i).delete("\n"))
  end
end

#parse_this_gff_file(i) ⇒ Object

#

parse_this_gff_file

Use this method if you wish to parse a .gff or .gff3 file.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7117

def parse_this_gff_file(i)
  if i.is_a? Array
    i.each {|entry| parse_this_gff_file(entry) }
  else
    ::Bioroebe::Parser::GFF.new(i)
  end
end

#parse_this_pdb_file(i) ⇒ Object

#

parse_this_pdb_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 5738

def parse_this_pdb_file(i)
  ParsePdbFile.new(i)
end

#parse_this_user_input(i) ⇒ Object

#

parse_this_user_input

This method will always reset the user-input specific variables.

#


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# File 'lib/bioroebe/shell/shell.rb', line 782

def parse_this_user_input(i)
  reset_the_user_input_specific_variables
  # ======================================================================= #
  # Act on input that has at the least one ' ' character next.
  # ======================================================================= #
  if i.include? ' '
    splitted = i.split(' ')             
    @internal_hash[:command_to_be_passed_to_the_menu] = splitted[0]
    @internal_hash[:all_arguments]       = splitted[1 .. -1]
    @internal_hash[:first_argument]      = splitted[1]
    @internal_hash[:remaining_arguments] = splitted[2 .. -1] # Unsure if this is correct. 
  else
    @internal_hash[:command_to_be_passed_to_the_menu] = i
  end
end

#perform_a_pubmed_search(i) ⇒ Object

#
#


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# File 'lib/bioroebe/shell/shell.rb', line 1601

def perform_a_pubmed_search(i)
  if i.is_a? Array
    i = i.first
  end
  search_term = i.dup.delete('=')
  url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term='+
        search_term
  dataset = open(url).read
  # =================================================================== #
  # Grab the IDs next - this functionality is very unfinished as of
  # right now (December 2018):
  # =================================================================== #
  id_matches = dataset.scan(/<Id>\d+<\/Id>/)
  unless id_matches.empty?
    e
    erev 'The following '+sfancy(id_matches.size.to_s)+
         rev+' IDs were found:'
    e
    id_matches.each {|entry|
      erev '  '+sfancy(entry.delete('Id</>'))+rev
    }
    e
  end
end

#perform_frameshift_action(i) ⇒ Object

#

perform_frameshift_action

This method attempts to perform a frameshift on our target sequence. We can give, as argument, 1,2,+3 etc. Note that the + character is optional - if omitted, we assume that it was passed.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1952

def perform_frameshift_action(i)
  i = i.to_s
  if sequence?.empty?
    erev 'Please first "assign" a sequence before trying to'
    erev 'perform a frameshift on it.'
  else
    if i == 'all'
      erev 'We will perform all frameshift actions next.'
      perform_frameshift_action '+1'
      perform_frameshift_action '+2'
      perform_frameshift_action '+3'
    elsif i.to_i == 0
      report_syntax_help_for_frameshift_action
    else
      erev 'Performing a frameshift on our target sequence next.'
      erev 'The frameshift to perform will be '+simp(('+'+i).squeeze('+'))+'.'
      erev 'We will modify the main sequence directly.'
      sequence?[0, i.to_i] = ''
      show_main_string
    end
  end
end

#perform_startup_actions ⇒ Object

#

perform_startup_actions (startup tag)

Currently, the only startup-action we perform is to add to the statistics.yml file.

We must check whether we have proper permissions though.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1176

def perform_startup_actions
  # ======================================================================= #
  # Initialize the default stop codons, if they are empty.
  # ======================================================================= #
  if ::Bioroebe.stop_codons?.empty?
    ::Bioroebe.initialize_default_stop_codons
  end
  # ======================================================================= #
  # The next line must come after we checked for the commandline arguments,
  # so that options such as --disable-colours are properly handled.
  # ======================================================================= #
  consider_assigning_the_default_dna_sequence_from_a_yaml_file
  # ======================================================================= #
  # === Handle statistics next
  # ======================================================================= #
  _ = Bioroebe.file_statistics? # Assign a shorter handle to it.
  _ = bioshell_log_dir?+File.basename(_)
  # ======================================================================= #
  # We must check here if we can write into the base directory.
  # ======================================================================= #
  base_directory = File.dirname(_)
  if File.writable?(base_directory)
    if File.exist? _ # If it exists, add one to it.
      what = YAML.load_file(_)
      what[:n_times] = what[:n_times]+1
      write_what_into(YAML.dump(what), _)
    else # else the file does not yet exist, so we create it.
      hash = { n_times: 1 }
      write_what_into(YAML.dump(hash), _)
      if may_we_show_the_startup_information?
        show_startup_information
      end
    end
  else
    e "Can not write into the directory `#{sdir(base_directory)}`."
  end
  ensure_that_the_bioshell_log_directory_exists
  consider_analysing_the_local_dataset_on_startup # Should come after the log-directory-exists check.
  check_for_local_vectors # Also check for local vectors, such as pBR322 datasets stored in fasta files.
  considering_changing_the_title_of_the_kde_konsole_tab
  if is_on_roebe?
    if dna_sequence?.nil? or
       dna_sequence?.empty?
      # =================================================================== #
      # On my home system, we use a sequence of 150 by default.
      # =================================================================== #
      set_dna_sequence(150, :be_quiet)
    end
  end
end

#permanently_disable_startup_intro ⇒ Object

#

permanently_disable_startup_intro

This method can be used to permanently disable the startup intro.

Invocation example:

bioshell --permanently-disable-startup-intro
#


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# File 'lib/bioroebe/shell/shell.rb', line 6263

def permanently_disable_startup_intro
  target_file = Bioroebe.project_base_dir?+
                'shell/configuration/may_we_show_the_startup_information.yml'
  what = 'false'
  write_what_into(what, target_file)
  erev 'Storing into the file '+sfile(target_file)+rev+'.'
  if is_on_roebe?
    target_file = RUBY_SRC+
                  'bioroebe/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml'
    write_what_into(what, target_file)
    erev 'Storing into the file '+sfile(target_file)+rev+'.'
  end
end

#prepend(i) ⇒ Object

#

prepend

You can use this to simply prepend to the main string.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5805

def prepend(i)
  sequence?.prepend(i)
end

#primer(i) ⇒ Object

#

primer?

#


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# File 'lib/bioroebe/shell/shell.rb', line 3779

def primer(i)
  i = i.to_s
  if i.empty?
    erev 'Please provide a number, which is the length of the Primer.'
  else
    erev 'We will design two primers, with a '\
         'length of '+i+rev+' each.'
    report_sequence
    _ = sequence?[0, i.to_i]
    reverse_sequence = sequence?.reverse[0, i.to_i]
    forward_primer = leading_three_prime+
                     rev+
                     sfancy(
                       complement(reverse_sequence.reverse)
                     )+rev+trailing_five_prime+
                     rev
    reverse_primer = leading_five_prime+
                     sfancy(
                       complement(_.reverse)
                     )+rev+trailing_three_prime+
                     rev
    erev 'Forward primer: '+forward_primer
    erev 'Reverse primer: '+reverse_primer
    e
    padding = ' ' * (sequence?.size.to_i - _.size)
    erev '  '+padding+forward_primer
    show_sequence # This is the main sequence.
    spacer = '|' * sequence?.size.to_i
    erev "       #{swarn(spacer)} #{rev}" 
    erev '  '+leading_three_prime+rev+
         sfancy(complement(sequence?))+rev+trailing_five_prime+rev
    erev '  '+leading_five_prime+rev+
         sfancy(_.to_s)+rev+
         trailing_three_prime+rev
    e
  end
end

#print_aa_table(optional_arguments = all_arguments?) ) ⇒ Object

#

print_aa_table

Use this method to print an overview over the aminoacid sequence that was assigned.

#


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# File 'lib/bioroebe/shell/shell.rb', line 979

def print_aa_table(optional_arguments = all_arguments?)
  require 'bioroebe/aminoacids/display_aminoacid_table.rb'
  if optional_arguments.is_a?(Array) and !optional_arguments.empty?
    _ = optional_arguments
  else
    _ = aminoacids?
  end
  _ = _.first if _.is_a? Array
  Bioroebe::DisplayAminoacidTable.new(_)
end

#print_aminoacid_information_table ⇒ Object

#

print_aminoacid_information_table

This method will give us as much information as possible about the various different aminoacids in the assumed protein sequence at hand.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4184

def print_aminoacid_information_table
  show_mnemo
  e
  show_aminoacids_mass_table # This will also report the average weight of an aminoacid.
  e
  show_aminoacids_residues # Show all aminoacid residues (the "Reste").
  e
  display_all_aminoacids
  e
end

#print_rev ⇒ Object

#

print_rev

#


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# File 'lib/bioroebe/shell/shell.rb', line 7520

def print_rev
  print rev
end

#protein_stats ⇒ Object

#

protein_stats

#


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# File 'lib/bioroebe/shell/shell.rb', line 6045

def protein_stats
  e
  e 'CURRENTLY NOT IMPLEMENTED'
  e
end

#pubmed(number = 125512) ⇒ Object

#

pubmed

Open a pubmed citation stuff.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4730

def pubmed(
    number = 125512
  )
  if number.is_a? Array
    number = number.join(' ').strip
  end
  use_this_url = 'https://pubmed.ncbi.nlm.nih.gov/'.dup
  if number and !number.nil?
    use_this_url << '?term='+number.to_s
  end
  ::Bioroebe.open_in_browser(use_this_url)
end

#punnet(i) ⇒ Object

#

punnet

This method will show a Punnet square.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3195

def punnet(i)
  ::Bioroebe::Punnet.new(i)
end

#purge(i) ⇒ Object

#

purge

This method can be used to purge nucleotides. E. g. if you want to get rid of all Thymines.

To invoke this method, do:

purge thymines
#


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# File 'lib/bioroebe/shell/shell.rb', line 4678

def purge(i)
  if i.nil?
    erev 'Please provide some input such as "thymine" or "t".'
    return
  end
  if i.is_a? Array
  else
    erev "Now purging all #{simp(i)}#{rev}:"
    case i
    when 'thymine','thymines'
      i = 'T'
    when 'cytosine','cytosines'
      i = 'C'
    when 'guanine','guanines'
      i = 'G'
    end
    new_string = sequence?.tr(i.upcase, '')
    set_sequence(new_string)
    show_string
  end
end

#random(n_elements = default_length?, , dna_or_amino_acid = :dna, do_report_the_sequence = false) ⇒ Object

#

random (random tag, rand tag)

This will generate a random DNA sequence or a random aminoacid sequence.

The first argument tells us how many nucleotides or amino acids should be part of that sequence.

If a second argument was given, we will generate AA. Otherwise we will generate DNA (which is the default).

Usage examples:

random dna
random dna 20
random 2552
random 2552 aa
#


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# File 'lib/bioroebe/shell/shell.rb', line 2744

def random(
    n_elements             = default_length?,
    dna_or_amino_acid      = :dna,
    do_report_the_sequence = false
  )
  if dna_or_amino_acid.is_a?(Array) and dna_or_amino_acid.empty?
    dna_or_amino_acid = :dna
  end
  # ====================================================================== #
  # === First handle Arrays
  # ====================================================================== #
  if dna_or_amino_acid.is_a? Array
    dna_or_amino_acid = dna_or_amino_acid.first
  end
  case n_elements.to_s
  # ====================================================================== #
  # === aminoacids
  # ====================================================================== #
  when 'aminoacids',
       /^aa$/i
    five_steps_array = [] # An array from 5 to 50, in 5 steps.
    5.step(50, 5) { |entry| five_steps_array << entry }
    n_elements = 200+five_steps_array.sample
    dna_or_amino_acid = :aminoacids
  # ====================================================================== #
  # === do_not_show_the_string
  # ====================================================================== #
  when 'do_not_show_the_string'
    dna_or_amino_acid = :dna
    n_elements = default_length?
    do_report_the_sequence = false
  # ====================================================================== #
  # === dna
  # ====================================================================== #
  when 'dna','' # This also handles nil.
    n_elements = default_length?
    if only_numbers?(dna_or_amino_acid)
      n_elements = dna_or_amino_acid.to_i
    end
    dna_or_amino_acid = :dna
  # ====================================================================== #
  # === nil
  # ====================================================================== #
  when nil
    n_elements = default_length? # defaults to 1000.
  end
  # ====================================================================== #
  # If input has NOT only numbers alone:
  # ====================================================================== #
  if n_elements.to_s !~ /^\d+$/
    n_elements = default_length?
  end
  dna_or_amino_acid = dna_or_amino_acid.to_s
  # ====================================================================== #
  # === Handle DNA or amino acid as input next
  # ====================================================================== #
  case dna_or_amino_acid
  # ====================================================================== #
  # === dna
  # ====================================================================== #
  when 'dna',
       'd',
       'default',
       ''
    # '' is also the default for this.
    # ==================================================================== #
    # Delegate towards the main setter next. 
    # ==================================================================== #
    set_DNA_sequence(n_elements)
  # ====================================================================== #
  # === aminoacids
  # ====================================================================== #
  when 'aminoacids',
       'aminoacid',
       'aa'
    e 'Generating some ('+sfancy(n_elements.to_s)+rev+') AminoAcids next.'
    _ = set_aminoacids(:generate, n_elements, :be_silent) # We are silent here because we report lateron anyway.
    output = _
  end
  # ======================================================================= #
  # Next, show this string if we also wish to report the sequence.
  # ======================================================================= #
  show_string(output) if do_report_the_sequence
  return _ # Last but not least, return it.
end

#random_dna_sequence(length = 250) ⇒ Object

#

random_dna_sequence

Generate a random DNA sequence. Note that this will return a String - if you wish to put this onto a Sequence object then you have to handle this situation on your own.

The argument shall be how many DNA nucleotides you want to have.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5134

def random_dna_sequence(
    length = 250
  )
  ::Bioroebe.generate_random_dna_sequence(length)
end

#random_insert(i) ⇒ Object

#

random_insert

Use this method to do a random insert into your main DNA sequence.

The input should be a nucleotide sequence such as ATGCCA, but it can also be a number - see the examples below for that.

Note that this method will insert the given input into ONE random position of our main sequence.

To use this, try:

random 15; rinsert ATTGGGCCC
random 15; rinsert 5
random 15; rinsert 15
#


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# File 'lib/bioroebe/shell/shell.rb', line 3344

def random_insert(i)
  i = i.join if i.is_a? Array
  i.delete!(' ')
  if i =~ /\d+$/ # If it has at the least one number.
    _ = ''.dup
    i.to_i.times { _ << return_random_nucleotide }
    e "The #{simp(i.to_i.to_s)}#{rev} nucleotides to be added "\
      "will be `#{sfancy(_)}#{rev}`."
    i = _
  end
  # ======================================================================= #
  # We need to determine the insert position. The insert_position can
  # be 0 zoo.
  # ======================================================================= #
  insert_position = rand(sequence?.size)
  n_nucleotides = i.size.to_s
  e 'Inserting '+sfancy(n_nucleotides.to_s)+rev+' nucleotides at '\
    'nucleotide position '+simp(insert_position.to_s)+rev+'.'
  old_size = sequence?.size
  sequence?[insert_position+1, 0] = i
  e 'The old size was '+sfancy(old_size.to_s)+
     rev+'. The new size is '+
     sfancy(sequence?.size.to_s)+
     rev+'.'
end

#raw_aminoacid_sequence? ⇒ Boolean Also known as: aminoacids?, amino_acid_sequence?, aminoacid_sequence?, aa_sequence?, aa?

#

raw_aminoacid_sequence?

Reader method over the aminoacid sequence.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 880

def raw_aminoacid_sequence?
  @internal_hash[:array_aminoacid_sequence].last
end

#raw_sequence? ⇒ Boolean Also known as: dna_sequence_as_string?, dna_sequence_object_as_string?, sequence_as_string?

#

raw_sequence?

This method must always return a String.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 846

def raw_sequence?
  # @internal_hash[:nucleotide_sequence].to_s
  @internal_hash[:array_dna_sequences].last.to_str
end

#readline_is_available? ⇒ Boolean Also known as: use_readline?, has_readline?

#

readline_is_available?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/readline.rb', line 74

def readline_is_available?
  ::Bioroebe.readline_is_available? # Query the constant value in this case.
end

#register_this_download(i) ⇒ Object

#

register_this_download

Simply register all downloads - we may use this information at some later point.

The entries here typically are HTTP or HTTPS-URLs.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10263

def register_this_download(i)
  @internal_hash[:array_all_downloads] << i
end

#remaining_arguments? ⇒ Boolean

#

remaining_arguments?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7431

def remaining_arguments?
  @internal_hash[:remaining_arguments]
end

#remove_question_mark? ⇒ Boolean

#

remove_question_mark?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7304

def remove_question_mark?
  @internal_hash[:remove_last_character_if_it_is_a_question_mark]
end

#remove_sequence(i) ⇒ Object Also known as: remove

#

remove_sequence

Use this method to chop away from the beginning part of a nucleotide sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3017

def remove_sequence(i)
  i = i.first if i.is_a? Array
  i = i.to_i
  if dna_sequence_as_string?.size == 0
    erev 'Can not remove any more characters as we do not have a '\
         'sequence anymore.'
  else
    erev "Removing #{sfancy(i)}#{rev} characters from the "\
         "start (left side; 5' end)."
    _ = dna_sequence?
    _.remove_n_characters_from_the_left_side(i)
    this_sequence = _
    set_dna_sequence(this_sequence)
  end
end

#remove_trailing_escape_code(i) ⇒ Object

#

remove_trailing_escape_code

#


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# File 'lib/bioroebe/shell/shell.rb', line 147

def remove_trailing_escape_code(i)
  return i unless use_colours?
  ::Colours.remove_trailing_escape_code(i)
end

#replay(i = nil) ⇒ Object

#

replay

#


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# File 'lib/bioroebe/shell/shell.rb', line 11099

def replay(i = nil)
  if i
    # ===================================================================== #
    # The user did input something. Thus continue here.
    # ===================================================================== #
    case i
    # ===================================================================== #
    # === save
    # ===================================================================== #
    when 'save',
         'store'
      verbose_save_history_to_file
    else
      # =================================================================== #
      # Else load the replay file. For instance, via "replay load".
      # =================================================================== #
      replay_file = log_dir?+'replay_file.yml'
      if File.exist? replay_file
        erev 'Now replaying the history from the file `'+sfile(replay_file)+rev+'`.'
        array = YAML.load_file(replay_file)
        array.each {|command|
          run_this_user_input(command)
        }
      else
        erev 'We are trying to replay the old history, but we could not find'
        erev 'any file called '+sfile(replay_file)+'.'
        e
        erev 'You can generate a new replay file by inputting some commands'
        erev 'and then invoking "replay".' 
      end
    end
  else
    verbose_save_history_to_file
  end
end

#report_all_stop_codons(i = dna_sequence_object? ) ⇒ Object

#

report_all_stop_codons

This method will report all stop codons in the given sequence.

We will not modify the input given to this method.

The three stop codons, in RNA, are:

UGA
UAG
UAA
#


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# File 'lib/bioroebe/shell/shell.rb', line 1517

def report_all_stop_codons(
    i = dna_sequence_object?
  )
  i.upcase!
  erev 'Our input sequence has '+simp(i.size.to_s)+rev+' nucleotides.'
  n_UGA = 'UGA'
  n_UGA = 'TGA' if is_dna?
  erev 'We did find '+
        simp(
          i.scan(/#{n_UGA}/
        ).size.to_s.rjust(2))+rev+' '+n_UGA+' stop codons.'
  n_UAG = 'UAG'
  n_UAG = 'TAG' if is_dna?
  erev 'We did find '+
        simp(i.scan(/#{n_UAG}/).size.to_s.rjust(2))+rev+' '+n_UAG+' stop codons.'
  n_UAA = 'UAA'
  n_UAA = 'TAA' if is_dna?
  erev 'We did find '+
        simp(i.scan(/#{n_UAA}/).size.to_s.rjust(2))+rev+' '+n_UAA+' stop codons.'
end

#report_colourized_sequence(colourize_what = :start_and_stop_codon) ⇒ Object

#

report_colourized_sequence

This method will use the new class ColourizeSequence, rather than the old internal way.

In the long run, it may be best to transition all of the Bioroebe::Shell into the new class - but for now, we will use a hybrid system.

To invoke this method, try:

start_and_stop?
#


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# File 'lib/bioroebe/shell/shell.rb', line 1260

def report_colourized_sequence(
    colourize_what = :start_and_stop_codon
  )
  _ = ColourizeSequence.return_sequence(dna_sequence_object?) { colourize_what }
  show_nucleotide_sequence?.display(_)
  e
end

#report_current_genbank_version(optional_arguments = nil) ⇒ Object

#

report_current_genbank_version

You can use this method to report the current genbank version.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6621

def report_current_genbank_version(
    optional_arguments = nil
  )
  remote_url = 'https://www.ncbi.nlm.nih.gov/genbank/statistics/'
  if optional_arguments
    case optional_arguments
    when :also_report_the_URL
      erev 'We will obtain the latest Genbank version from the URL:'
      e
      erev "  #{simp(remote_url)}"
      e
    end
  end
  remote_dataset = URI.open(remote_url).read.split(N)
  # ======================================================================= #
  # For the following Regex, see this link:
  #
  #   https://rubular.com/r/XC97c7i6sR
  #
  # ======================================================================= #
  regex_to_use =
    /<td>(\d{1,3})<\/td><td>(.{1,3}\s{1,3}\d{4})<\/td><td>\d+<\/td><td>\d+<\/td><td>\d+<\/td><td>\d+<\/td><\/tr><\/tbody><\/table>$/
  _ = ''.dup
  is_open = false
  remote_dataset.each {|line|
    if line.include? '<table id="stats_table" summary="GENBANK AND WGS'
      _ << line
      is_open = true
    else
      _ << line if is_open
      if line.include? '</table>'
        is_open = false
      end
    end
  }
  _ =~ regex_to_use # Match the regex against the substring assigned to _.
  version        = $1.to_s.dup
  month_and_year = $2.to_s.dup
  erev 'The current Genbank version is: '+simp(version)+
       rev+' (released on '+simp(month_and_year)+rev+')'
end

#report_current_working_directory ⇒ Object

#

report_current_working_directory

#


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# File 'lib/bioroebe/shell/shell.rb', line 4023

def report_current_working_directory
  _ = "We are in the directory:\n\n".dup
  _ << "  #{sdir(return_working_directory)}\n\n"
  e _
end

#report_everything_about_this_amino_acid(i) ⇒ Object

#

report_everything_about_this_amino_acid

Use this method to report everything about any particular amino acid.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7696

def report_everything_about_this_amino_acid(i)
  if i.is_a? Array
    i.each {|entry| report_everything_about_this_amino_acid(entry) }
  else
    i.delete!('?') if i.include? '?'
    erev 'It seems as is we did find an Amino Acid ('+simp(i)+rev+
         '). Its characteristic residue (R) is:'+N+N
    unless AMINO_ACIDS_RESTE.has_key?(i)
      # =================================================================== #
      # This here is to map german names, such as "glycin",
      # onto "glycine", the corresponding english name.
      # =================================================================== #
      if AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.has_key?(i)
        i = AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER[i]
        i = AMINO_ACIDS_ENGLISH[i].downcase
      end
    end
    residue = AMINO_ACIDS_RESTE[i.downcase].to_s
    efancy "  #{residue}#{N}"
    erev 'The codons coding for the aminoacid '+simp(i)+rev+' are:'
    e
    e '  '+mediumturquoise(
        ::Bioroebe::PossibleCodonsForThisAminoacid.new(i).pretty_result
      )
    e
    molecular_mass_of(i, 2) # The 2 says to round to 2 digit.
  end
end

#report_five_prime_three_prime(i) ⇒ Object

#

report_five_prime_three_prime

#


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# File 'lib/bioroebe/shell/shell.rb', line 7728

def report_five_prime_three_prime(i)
  erev dna_with_ends(i)
end

#report_how_many_aminoacids_we_have ⇒ Object

#

report_how_many_aminoacids_we_have

This method will report how many aminoacids we have assigned.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2486

def report_how_many_aminoacids_we_have
  if aminoacids?
    n_aminoacids = aminoacids?.size
  else
    n_aminoacids = dna_sequence_object?.size / 3.0
  end
  n_aminoacids = n_aminoacids.to_i
  erev "This sequence has #{simp(n_aminoacids.to_s)}#{rev} aminoacids."
end

#report_main_sequence(input = dna_sequence_as_string?, , colourize = nil) ⇒ Object Also known as: show_main_sequence, show_colourized_sequence, show_dna_sequence, show_DNA_sequence

#

report_main_sequence

We will call dna_with_ends() here in this method. The argument colourize will determine whether we will colourize the DNA strand or not.

Invocation examples:

report_main_sequence(::Bioroebe.start_codon?)
report_main_sequence(:start_codon) # ← is the same as the ^^^ above
report_main_sequence(:stop_codon)  # ← Colourize the stop-codons.
#


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# File 'lib/bioroebe/shell/shell.rb', line 1303

def report_main_sequence(
    input     = dna_sequence_as_string?,
    colourize = nil
  )
  case input
  # ======================================================================= #
  # === :stop_codon
  # ======================================================================= #
  when :stop_codon
    colourize = stop_codons?
    input     = dna_sequence_as_string?
  end
  original_input = input.dup
  case colourize
  # ======================================================================= #
  # === :stop_codon
  #
  # We attempt to colourize the stop-codons via this method.
  # ======================================================================= #
  when :stop_codon
    colourize = stop_codons?
  # ======================================================================= #
  # === :stop_codon_in_frame1
  # ======================================================================= #
  when :stop_codon_in_frame1,
       :stop_codon_in_frame2,
       :stop_codon_in_frame3
    new_string = remove_trailing_escape_code(
      colour_for_nucleotides(
        ''.dup
      ).dup
    ).dup
    n_stop_codons_were_found = 0
    prepend_this = ''.dup
    input = input.dup # Work on a copy here.
    case colourize
    when :stop_codon_in_frame2
      prepend_this << input[0,1]
      input[0,1] = ''
    when :stop_codon_in_frame3
      prepend_this << input[0,2]
      input[0,2] = ''
    end
    new_string << prepend_this
    scanned = input.scan(/.../) # Get a group of codons here.
    scanned.each {|codon|
      if is_a_stop_codon? codon
        n_stop_codons_were_found += 1
        new_string << colour_for_stop_codon(codon.dup).dup+
                      remove_trailing_escape_code(
                        colour_for_nucleotides
                      )
      else
        new_string << codon.dup
      end
    }
    case colourize
    # ===================================================================== #
    # === :stop_codon_in_frame2
    # ===================================================================== #
    when :stop_codon_in_frame2
      new_string << input[-2,2]
    # ===================================================================== #
    # === :stop_codon_in_frame3
    # ===================================================================== #
    when :stop_codon_in_frame3
      new_string << input[-1,1]
    end
    
    e "#{padding?}"\
      "#{rev}"\
      "#{leading_five_prime}"\
      "#{new_string}"\
      "#{rev}"\
      "#{trailing_three_prime}"
    erev "#{steelblue(n_stop_codons_were_found)} #{rev}stop "\
         "codons were found in this sequence of #{original_input.size} "\
         "nucleotides."
    return
  # ======================================================================= #
  # === :start_codon
  # ======================================================================= #
  when :start_codon # Instruction to use a start codon here.
    colourize = start_codon?
  # ======================================================================= #
  # === :start_and_stop_codon
  # ======================================================================= #
  when :start_and_stop_codon
    colourize = [start_codon?, stop_codons?]
  end
  # ======================================================================= #
  # The old code was:
  #
  #   erev padding?+
  #        dna_with_ends(input, colourize) { :honour_coding_area_if_it_exists } # The dna_with_ends() method can deal with Arrays.
  #
  # This is now mostly ported (April 2020), but the :honour_coding_area_if_it_exists
  # is not yet ported, so the above code will remain as-is, for the time
  # being.
  # ======================================================================= #
  if run_in_GUI_settings?
    set_result(
      five_leader?+
      input+
      three_trailer?
    )
  else
    show_nucleotide_sequence?.report_this_sequence(input) {{
      padding_to_use:             padding?,
      colourize_this_subsequence: colourize,
      use_colours:                use_colours?
    }}
  end
end

#report_mode ⇒ Object

#

report_mode

#


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# File 'lib/bioroebe/shell/shell.rb', line 11138

def report_mode
  erev mode?
end

#report_n_proteins_registered_in_swiss_prot ⇒ Object

#

report_n_proteins_registered_in_swiss_prot

This method will report how many proteins are registered in swiss-prot.

Invoke this method like so:

swiss-prot?
#


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# File 'lib/bioroebe/shell/shell.rb', line 2424

def report_n_proteins_registered_in_swiss_prot
  regex_to_use = /contains (\d+) sequence entries/ # See: http://rubular.com/r/Bl9tHfheEx
  url = 'https://web.expasy.org/docs/relnotes/relstat.html'
  dataset = open(url).read
  dataset =~ regex_to_use
  n_registered_proteins = $1.to_s.dup
  erev 'There are '+simp(n_registered_proteins)+rev+' registered '\
       'proteins in the Swiss-Prot database.'
  erev "The URL used to determine this was: "\
       "#{simp(url)}"
end

#report_n_start_codons(this_string = string?, , use_this_as_start_codon = :default, in_which_frame = :frame1) ⇒ Object

#

report_n_start_codons

Use this method to count how many ATG codons we have. We will honour the default start_codon in use.

The third argument determines which reading frame is to be used. By default, the method will use the first reading frame.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5386

def report_n_start_codons(
    this_string             = string?,
    use_this_as_start_codon = :default, # Use the proper start codon.
    in_which_frame          = :frame1
  )
  case use_this_as_start_codon
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    use_this_as_start_codon = ::Bioroebe.start_codon?
  end
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    when /^frame/
      in_which_frame = yielded.to_sym
    end
  end
  # ======================================================================= #
  # The following can be invoked via:
  #   n_ORF? frame1
  # ======================================================================= #
  case in_which_frame
  # ======================================================================= #
  # === :frame1
  # ======================================================================= #
  when :frame1
    in_which_frame = 'frame 1'
  # ======================================================================= #
  # === :frame2
  # ======================================================================= #
  when :frame2
    in_which_frame = 'frame 2'
  # ======================================================================= #
  # === :frame3
  # ======================================================================= #
  when :frame3
    in_which_frame = 'frame 3'
  end
  n_start_codons = this_string.upcase.scan(
    /#{use_this_as_start_codon}/
  ).size.to_s
  # ======================================================================= #
  # The above is not yet in the proper frame, though.
  # ======================================================================= #
  trailing_message = " Initiation Codons "\
                     "(in #{orangered(in_which_frame)}#{rev})."
  erev "Our main string has #{sfancy(n_start_codons)}#{rev}"\
       " #{simp(use_this_as_start_codon)}#{rev} ("\
       "#{use_this_as_start_codon.tr('T','U')})"+
       trailing_message
  if coding_area? # This has been user-supplied in that case.
    erev 'However had, only the nucleotides from position'
    erev "#{sfancy(coding_area?.to_s.split('..').first.to_s)}#{rev}"\
         " to position #{sfancy(coding_area?.to_s.split('..').last.to_s)}"\
         "#{rev} will be colourized."
  end
end

#report_size_of(i = nil) ⇒ Object

#

report_size_of

#


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# File 'lib/bioroebe/shell/shell.rb', line 9504

def report_size_of(
    i = nil
  )
  if i.nil?
    i = dna_sequence_object?
  end
  if i
    erev "This sequence contains #{sfancy(i.size.to_s)}#{rev} nucleotides."
  else
    report_size_of_main_string
  end
end

#report_size_of_main_string(i = dna_sequence_object?, , type_of_string = 'main ') ⇒ Object Also known as: report_length_of_the_dna_string, report_size_of_this_sequence

#

report_size_of_main_string

#


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# File 'lib/bioroebe/shell/shell.rb', line 7785

def report_size_of_main_string(
    i              = dna_sequence_object?,
    type_of_string = 'main ' # This is usually the main DNA string.
  )
  i = dna_sequence_object? if i.nil?
  i = dna_sequence_object? if i.is_a?(Array) and i.empty?
  erev 'The '+type_of_string+'string has '+sfancy(i.size.to_s)+
       rev+' '+nucleotides_or_aminoacids?+'.'
end

#report_syntax_help_for_frameshift_action ⇒ Object

#

report_syntax_help_for_frameshift_action

#


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# File 'lib/bioroebe/shell/shell.rb', line 1154

def report_syntax_help_for_frameshift_action
  result = <<-EOF

#{rev} You can provide these options for the frameshifting menu:

+1
+2
+3
all

EOF
  e result
end

#report_that_a_string_must_be_assigned_first ⇒ Object

#

report_that_a_string_must_be_assigned_first

#


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# File 'lib/bioroebe/shell/shell.rb', line 6403

def report_that_a_string_must_be_assigned_first
  erev 'No sequence has been assigned yet. Please first "'+
       sfancy('assign')+rev+'" a string.'
end

#report_that_the_main_sequence_is_frozen ⇒ Object

#

report_that_the_main_sequence_is_frozen

#


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# File 'lib/bioroebe/shell/shell.rb', line 2986

def report_that_the_main_sequence_is_frozen
  erev 'The main sequence is frozen and can not be modified '\
       'anymore.'
  erev 'You can "'+steelblue('unfreeze')+rev+
       '" it again, if you want to.'
end

#report_the_first_atg ⇒ Object

#

report_the_first_atg

This method will simply report the first ATG codon.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1137

def report_the_first_atg
  dna_sequence = dna_sequence_object_as_string?
  array_matches = ::Bioroebe.return_all_substring_matches(
    dna_sequence, start_codon?
  )
  start_position = array_matches.first.first
  erev 'The first ATG can be found at position '+
        simp(start_position.to_s)+rev+'.'
  erev 'We will next show the first 100 nucleotides, starting from this:'
  report_five_prime_three_prime(
    dna_sequence_object?[start_position-1,100]
  )
end

#report_the_protein_weight ⇒ Object

#

report_the_protein_weight

#


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# File 'lib/bioroebe/shell/shell.rb', line 8434

def report_the_protein_weight
  _ = aminoacid_sequence?
  if _.include? '*'
    erev 'Note that this aminoacid sequence has a stop codon, '\
         'denoted by the *:'
    e
    erev "  #{sfancy(_)}#{rev}"
    e
    erev 'Since a stop codon is not translated into an aminoacid'
    erev 'it makes little sense to include it into the weight-calculation.'
    erev 'Thus, we will use only the part up to the first * token.'
    _ = _[0 .. (_.index('*') - 1)]
  end
  sum = ::Bioroebe.amino_acid_average_mass(_)
  e 'The total weight of these '+simp(_.size.to_s)+rev+
    ' aminoacids is: '+sfancy(sum.to_f.round(2).to_s)+rev+
    ' Dalton'
end

#report_this_dna_sequence_with_proper_trailer_and_leader(i) ⇒ Object

#

report_this_dna_sequence_with_proper_trailer_and_leader

#


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# File 'lib/bioroebe/shell/shell.rb', line 1002

def report_this_dna_sequence_with_proper_trailer_and_leader(i)
  i = i.to_s
  if block_given?
    yielded = yield
    case yielded
    when :try_to_colourize_start_codon
      # =================================================================== #
      # We will try to colourize the start codon here.
      # =================================================================== #
      if i.start_with? start_codon?
        i[0,3] = cyan(i[0,3])+return_colour_for_nucleotides
      end
    end
  end
  colourized_dna_sequence = colourize_this_dna_sequence(i)
  colourized_dna_sequence = remove_trailing_escape_code(
    colourized_dna_sequence
  )
  erev left_pad?+
       leading_5_prime+
       colourized_dna_sequence+
       rev+
       trailing_3_prime
end

#report_this_input_was_not_found(i = '') ⇒ Object

#

report_this_input_was_not_found

This method is used to notify the user that a certain input was not found.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9804

def report_this_input_was_not_found(
    i = ''
  )
  unless i.empty?
    erev "Input `#{sfancy(i.to_s)}#{rev}` was not "\
         "found to be a valid input for the BioShell."
  end
end

#report_useful_packages_installed ⇒ Object

#

report_useful_packages_installed

This aggregate method can be used to report versions that may be installed on the given system, e. g. science-based projects and similar variants.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6325

def report_useful_packages_installed
  try_to_report_the_version_of_viennarna
  try_to_report_the_version_of_bedtools
end

#report_when_the_bioroebe_project_was_last_updated ⇒ Object

#

report_when_the_bioroebe_project_was_last_updated

#


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# File 'lib/bioroebe/shell/shell.rb', line 7863

def report_when_the_bioroebe_project_was_last_updated
  result = 'The Bioroebe-Project was last updated on: '+
            slateblue(LAST_UPDATE)+rev
  result = result.dup
  n_days_difference = ((Time.now - Time.parse(LAST_UPDATE))/60/60/24).round(2).to_s
  result << ' (~'+n_days_difference.to_s+' days ago)'
  erev result
end

#report_where_the_home_directory_can_be_found(i = log_dir? ) ⇒ Object

#

report_where_the_home_directory_can_be_found

#


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# File 'lib/bioroebe/shell/shell.rb', line 1786

def report_where_the_home_directory_can_be_found(
    i = log_dir?
  )
  erev 'The "home" directory (actually called the log directory) '\
       'can be found here:'
  e
  e "  #{sdir(i)}"
  e
end

#report_where_the_pdf_tutorial_can_be_found ⇒ Object

#

report_where_the_pdf_tutorial_can_be_found

Do notify the user where to find the .pdf tutorial.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5569

def report_where_the_pdf_tutorial_can_be_found
  _ = File.basename(FILE_BIOROEBE_TUTORIAL)
  erev 'You can find the tutorial here:'
  e
  erev '  '+simp('http://shevegen.square7.ch/'+_)+rev
  e
end

#report_where_we_store ⇒ Object

#

report_where_we_store

#


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# File 'lib/bioroebe/shell/shell.rb', line 5990

def report_where_we_store
  erev "We will store output from the Bioroebe-Project "\
       "into #{sfile(save_file?)}."
end

#report_whether_readline_is_available ⇒ Object

#

report_whether_readline_is_available

#


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# File 'lib/bioroebe/shell/shell.rb', line 4054

def report_whether_readline_is_available
  erev 'Is readline available? '+
    slateblue(
      verbose_truth(
        (Object.const_defined? :Readline)
      )
    )
end

#report_whether_we_will_make_use_of_expand_cd_aliases ⇒ Object

#

report_whether_we_will_make_use_of_expand_cd_aliases

#


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# File 'lib/bioroebe/shell/shell.rb', line 6314

def report_whether_we_will_make_use_of_expand_cd_aliases
  erev Bioroebe::VerboseTruth[use_expand_cd_aliases?]
end

#report_which_yaml_engine_is_in_use ⇒ Object

#

report_which_yaml_engine_is_in_use

#


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# File 'lib/bioroebe/shell/shell.rb', line 9495

def report_which_yaml_engine_is_in_use
  erev 'The yaml engine in use is: '+
       sfancy(::Bioroebe.use_which_yaml_engine?)+
       rev
end

#reset(be_verbose = true) ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/shell/shell.rb', line 406

def reset(
    be_verbose = true
  )
  super()
  infer_the_namespace
  reset_to_the_initial_state(be_verbose)
  # ======================================================================= #
  # Make sure that the base directories exist, within reset(). This
  # should come after reset_to_the_initial_state().
  # ======================================================================= #
  ensure_that_the_base_directories_exist
  # ======================================================================= #
  # Next, we have to try to enable the configuration.
  # ======================================================================= #
  enable_configuration # This should come after reset_to_the_initial_state().
  set_default_length # Set the default length of 1000 here.
end

#reset_the_user_input_specific_variables ⇒ Object

#

reset_the_user_input_specific_variables

#


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# File 'lib/bioroebe/shell/shell.rb', line 801

def reset_the_user_input_specific_variables
  @internal_hash[:all_arguments].clear
  @internal_hash[:remaining_arguments].clear
  @internal_hash[:first_argument] = nil
  # @internal_hash[:first_argument] = nil if @internal_hash.has_key?(:first_argument)
  @internal_hash[:command_to_be_passed_to_the_menu] = nil
  @internal_hash[:result].clear
end

#reset_to_the_initial_state(be_verbose = true) ⇒ Object Also known as: reset_to_the_internal_state

#

reset_to_the_initial_state

#


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# File 'lib/bioroebe/shell/shell.rb', line 427

def reset_to_the_initial_state(
    be_verbose = true
  )
  # ======================================================================= #
  # === :array_palindromes
  # ======================================================================= #
  @internal_hash[:array_palindromes] = []
  # ======================================================================= #
  # === :file_dna_string_saved
  #
  # Where to store our DNA string by default.
  # ======================================================================= #
  @internal_hash[:file_dna_string_saved] = "#{log_dir?}dna_string_saved.yml"
  # ======================================================================= #
  # === :array_jumper_directories
  # ======================================================================= #
  @internal_hash[:array_jumper_directories] = []
  # ======================================================================= #
  # === :array_fasta
  # ======================================================================= #
  @internal_hash[:array_fasta] = []
  # ======================================================================= #
  # === analyse_the_local_dataset_on_startup
  #
  # If this setting is set to true then, on startup, the bioshell
  # will report some information about the local dataset (FASTA
  # files and pdb files).
  # ======================================================================= #
  @internal_hash[:analyse_the_local_dataset_on_startup] = true
  # ======================================================================= #
  # === search_for
  # ======================================================================= #
  @internal_hash[:search_for] = nil
  # ======================================================================= #
  # === coding_area
  # ======================================================================= #
  @internal_hash[:coding_area] = nil # This can keep track of the real coding area.
  # ======================================================================= #
  # === misc_sequence
  # ======================================================================= #
  @internal_hash[:misc_sequence] = nil # This can store a misc DNA or RNA sequence.
  # ======================================================================= #
  # === :array_sequences
  # ======================================================================= #
  # @internal_hash[:array_sequences] = []
  # ======================================================================= #
  # === :registered_actions
  # ======================================================================= #
  @internal_hash[:registered_actions] = ARRAY_REGISTERED_ACTIONS
  # ======================================================================= #
  # === :result
  #
  # The content of this variable can be shown in the jruby-GUI for the
  # bioshell, for instance.
  # ======================================================================= #
  @internal_hash[:result] = ''.dup
  # ======================================================================= #
  # === :array_dna_sequence
  # ======================================================================= #
  @internal_hash[:array_dna_sequences] = []
  # ======================================================================= #
  # === :the_main_sequence_is_frozen
  # ======================================================================= #
  @internal_hash[:the_main_sequence_is_frozen] = false
  # ======================================================================= #
  # === :silent_startup
  #
  # This variable keeps track as to whether we will display a welcome
  # message on startup or whether we will not.
  # ======================================================================= #
  @internal_hash[:silent_startup] = false
  # ======================================================================= #
  # === :create_directories_on_startup_of_the_shell
  #
  # If this variable is set to true then the bio-shell will create
  # some directories on startup. The user can modify this from
  # the commandline, though, and specifically disable it.
  # ======================================================================= #
  @internal_hash[:create_directories_on_startup_of_the_shell] = true
  # ======================================================================= #
  # === array_history
  #
  # This array will keep track of the input-history, aka the commands
  # that the user has used.
  # ======================================================================= #
  @internal_hash[:array_history] = []
  # ======================================================================= #
  # === remove_last_character_if_it_is_a_question_mark
  #
  # If this variable is set to true then we will remove the last
  # input character - at the least if it is a '?'.
  # ======================================================================= #
  @internal_hash[:remove_last_character_if_it_is_a_question_mark] = false
  # ======================================================================= #
  # === :array_aminoacid_sequence
  #
  # This variable should be an empty Array, aka [], initially, so that we
  # can distinguish the case when the user has added data onto that
  # Array.
  # ======================================================================= #
  @internal_hash[:array_aminoacid_sequence] = []
  # ======================================================================= #
  # === exit_the_shell_how
  #
  # The next variable has two valid modes:
  #
  #   :instantly
  #   :exit_gracefully
  #
  # The first is the default; the second can be used if the Bioshell
  # is embedded into another program.
  # ======================================================================= #
  @internal_hash[:exit_the_shell_how] = :instantly
  # ======================================================================= #
  # === search_for
  #
  # This is the sequence we wish to find, in a given nucleotide sequence.
  # By default this will be nil.
  # ======================================================================= #
  @internal_hash[:search_for] = nil
  # ======================================================================= #
  # === show_the_leader
  # ======================================================================= #
  @internal_hash[:show_the_leader]  = true # Show the 5' leader.
  # ======================================================================= #
  # === show_the_trailer
  # ======================================================================= #
  @internal_hash[:show_the_trailer] = true # Show the 3' trailer.
  # ======================================================================= #
  # === :array_rna_sequence
  #
  # This can be populated with sequence objects such as:
  #
  #   Bioroebe::Sequence.new(''.dup, :rna)
  #
  # ======================================================================= #
  @internal_hash[:array_rna_sequences] = []
  # ======================================================================= #
  # === @save_file
  # ======================================================================= #
  @internal_hash[:save_file] = BIOSHELL_SAVE_FILE
  # ======================================================================= #
  # === @use_working_directory_as_prompt
  # ======================================================================= #
  @internal_hash[:use_working_directory_as_prompt] = false
  # ======================================================================= #
  # === @debug
  #
  # Determine whether we will debug or whether we will not
  # ======================================================================= #
  @internal_hash[:debug] = SHALL_WE_DEBUG
  # ======================================================================= #
  # === user_input
  # ======================================================================= #
  @internal_hash[:user_input] = nil
  # ======================================================================= #
  # === prompt_to_use
  #
  # This variable keeps track as to which prompt is to be used.
  # ======================================================================= #
  @internal_hash[:prompt_to_use] = :default
  # ======================================================================= #
  # === :use_xsel
  #
  # This method will determine whether we will use the external
  # program "xsel". By default, at the least on my home system,
  # I prefer to make use of xsel.
  # ======================================================================= #
  @internal_hash[:use_xsel] = true
  # ======================================================================= #
  # === @mode
  #
  # @mode can be either :dna or :rna or :aminoacid
  # ======================================================================= #
  @internal_hash[:mode] = :dna
  # ======================================================================= #
  # === @array_these_sequences_were_chopped_away
  #
  # Keep an Array that can be used to keep track of which sequences
  # were chopped away. Whenever we perform a chop-related action we
  # will store that sequence in an Array.
  # ======================================================================= #
  @internal_hash[:array_these_sequences_were_chopped_away] = []
  # ======================================================================= #
  # === array_timer_snapshots
  # ======================================================================= #
  @internal_hash[:array_timer_snapshots] = [] # This Array keeps track of the time.
  # ======================================================================= #
  # === may_we_show_the_startup_information
  #
  # This variable determines whether the startup-information may be
  # shown, on start-up of the bioshell. By default this will be true
  # typically, but a config-variable may overrule this.
  # ======================================================================= #
  @internal_hash[:may_we_show_the_startup_information] = true
  if @configuration and @configuration.respond_to? :may_we_show_the_startup_information
    @internal_hash[:may_we_show_the_startup_information] = @configuration.may_we_show_the_startup_information
  end
  # ======================================================================= #
  # === :show_nucleotide_sequence
  # ======================================================================= #
  @internal_hash[:show_nucleotide_sequence] = ::Bioroebe::ShowNucleotideSequence.new(
    '', :do_not_run_yet
  )
  # ======================================================================= #
  # === fasta_file
  #
  # This used to be a standalone @hash variable, but during the
  # rewrite in April 2020 this was integrated into @internal_hash.
  # ======================================================================= #
  @internal_hash[:fasta_file] = {}
  # ======================================================================= #
  # === @array_all_downloads
  # ======================================================================= #
  @internal_hash[:array_all_downloads] = [] # Must be an Array.
  # ======================================================================= #
  # === @use_working_directory_as_prompt
  # ======================================================================= #
  @internal_hash[:use_working_directory_as_prompt] = true
  # ======================================================================= #
  # === Determine whether silent startup is active
  #
  # Next, determine whether we will show a small startup-message or
  # whether we shall not show it. By default this should be false -
  # but if a file called 'use_silent_startup.yml' exists then we
  # will use that file.
  # ======================================================================= #
  if File.exist? FILE_USE_SILENT_STARTUP
    dataset = YAML.load_file(FILE_USE_SILENT_STARTUP)
    if dataset.is_a?(Hash) and dataset.has_key?('use_silent_startup')
      @internal_hash[:silent_startup] = dataset['use_silent_startup']
    end
  else # else it is 
    @internal_hash[:silent_startup] = false
  end
  # ======================================================================= #
  # === Enable the clipboard next:
  # ======================================================================= #
  initialize_clipboard
  # ======================================================================= #
  # === Setting towards a default padding
  #
  # Next comes left-padding, defaulting to '  '. This should come after
  # the clipboard has been initialized, and after @internal_hash has
  # been fully populated.
  # ======================================================================= #
  set_padding :default
  set_sequence_2
  set_sequence_3
  set_sequence_4
  set_sequence_5
  set_sequence_6
  ::Bioroebe.clear_array_colourize_this_aminoacid
  # ======================================================================= #
  # === :nucleotide_sequence
  # ======================================================================= #
  # @internal_hash[:nucleotide_sequence] = ::Bioroebe::Sequence.new
  # ======================================================================= #
  # === :sequence
  #
  # We set thesequence to a new instance of Bioroebe::Sequence next.
  # ======================================================================= #
  reset_string
  # ======================================================================= #
  # === :use_colours
  #
  # Let's enable the colours.
  # ======================================================================= #
  extended_enable_colours(:be_quiet)
  initialize_the_user_input_specific_variables
  set_runmode(:commandline) # Always have a default set.
end

#restore_default_prompt ⇒ Object

#

restore_default_prompt

#


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# File 'lib/bioroebe/shell/shell.rb', line 8677

def restore_default_prompt
  set_prompt :default
end

#restore_the_last_chop_operation ⇒ Object

#

restore_the_last_chop_operation

This method will “restore” the last chop operation.

Presently it will only append onto the 3’ area but in the future this may change, depending on whether we will store the position as well.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2557

def restore_the_last_chop_operation
  if @internal_hash[:array_these_sequences_were_chopped_away].empty?
    erev 'Can not restore the last chop-operation as we have not yet'
    erev 'chopped away any nucleotide from the main sequence.'
  else
    this_sequence = @internal_hash[:array_these_sequences_were_chopped_away].pop
    erev 'Now adding the sequence '+
         format_this_nucleotide_sequence(
           this_sequence
         )
    erev 'to our main sequence.'
    main_sequence?.append(this_sequence)
  end
end

#restriction_enzyme_digest(split_at = nil) ⇒ Object Also known as: digest

#

restriction_enzyme_digest

This method allows us to simulate a restriction digest, on a DNA polymer.

You can either give the matching DNA nucleotides or you can use the name of a restriction enzyme instead, such as ‘EcoRI’.

Usage examples:

random 750; digest_at TTGC
random 750; digest_at EcoRI
random 2000; [33,0] = GAATTC; digest_at EcoRI
#


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# File 'lib/bioroebe/shell/shell.rb', line 9431

def restriction_enzyme_digest(
    split_at = nil # Default value is nil.
  )
  _ = dna_sequence? # Keep a copy of the DNA sequence.
  # ======================================================================= #
  # === Grab the first entry if we have an Array
  # ======================================================================= #
  split_at = split_at.first if split_at.is_a? Array
  split_at = 'TTG' if split_at.nil?
  split_at = split_at.to_s # Work on Strings past this point here.
  split_at.sub!(/^first_/,'') if split_at.include? 'first_ATG'
  # ======================================================================= #
  # === Chop off all '?' in the sequence
  # ======================================================================= #
  split_at.delete!('?') if split_at.include? '?'
  # ======================================================================= #
  # Next, allow the user to substitute for names of restriction enzymes.
  # How do we determine that a restriction enzyme was given to this
  # method? Simple - we first remove all instances of 'A','T','C','G'
  # in our DNA sequence string. If the string is then still not empty,
  # we will assume that it is the name of a restriction enzyme.
  # ======================================================================= #
  unless (_.delete('ATGC').size > 0)
    erev 'Assumingly a restriction enzyme was given as input.'
    target_sequence = ::Bioroebe.restriction_enzyme(split_at)
    # Must check for nil values still
    if target_sequence
      erev "Substituting with `#{simp(target_sequence)}#{rev}` next (for #{split_at})."
      split_at = target_sequence
    else
      erev 'No substitute could be found for `'+sfancy(split_at)+rev+'`.'
    end
  end
  if _.include? split_at
    splitted = _.split(split_at)
    e
    erev 'We will next display all '+simp(splitted.size.to_s)+rev+
         ' segments that were found (in orange is the part that '\
         'is cut-out):'
    e
    splitted.each_with_index {|sequence, index|
      index += 1
      erev lpad?+lead_five_prime+sfancy(sequence)+rev+
           trail_three_prime+' (size: '+
           violet(sequence.size.to_s)+rev+')'
      unless index > (splitted.size-1)
        erev lpad?+lead_five_prime+orange(split_at)+rev+
          trail_three_prime+rev
      end
    }
    e
    erev 'Note that this will NOT be the actual DNA fragments, '\
         'because the restriction'
    erev 'enzyme may cut differentially within that orange sequence.'
  else # The target sequence was not included in this case.
    erev "No target match for `"\
         "#{simp(target_sequence)}#{rev}` was "\
         "found in the given DNA sequence."
  end
end

#restriction_enzymes_run ⇒ Object

#

restriction_enzymes_run

#


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# File 'lib/bioroebe/shell/shell.rb', line 4337

def restriction_enzymes_run
  require 'bioroebe/gui/gtk2/restriction_enzymes/restriction_enzymes.rb'
  ::Bioroebe::GUI::Gtk::RestrictionEnzymes.start_gui_application
end

#result? ⇒ Boolean

#

result?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 813

def result?
  @internal_hash[:result]
end

#return_a_random_sequence_of_n_nucleotides(i = 250) ⇒ Object

#

return_a_random_sequence_of_n_nucleotides

#


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# File 'lib/bioroebe/shell/shell.rb', line 2662

def return_a_random_sequence_of_n_nucleotides(
    i = 250
  )
  _ = ''.dup
  i.times {
    _ << return_random_nucleotide
  }
  return _
end

#return_all_genes ⇒ Object

#

return_all_genes

#


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# File 'lib/bioroebe/shell/shell.rb', line 8897

def return_all_genes
  _ = dna_sequence?
  result = _.to_enum(:scan, /(ATG|AUG)/i).map { |match|
    $`.size + 1 # +1 because we refer to the nucleotide positions.
  }
  e
  result.each_with_index {|nucleotide_position, index|
    erev simp(index+1).to_s+rev+') DNA sequence:'
    e
    sequence = _[nucleotide_position-1 .. -1]
    erev dna_with_ends(sequence, ::Bioroebe.start_codon?, 1)
    e
  }
end

#return_available_vectors ⇒ Object

#

return_available_vectors

#


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# File 'lib/bioroebe/shell/shell.rb', line 3060

def return_available_vectors
  Dir["#{::Bioroebe.log_dir?}vector_*"]
end

#return_complement(i = dna_sequence? ) ⇒ Object Also known as: complement, complement_sequence?, reverse

#

return_complement

This method is aliased to complement() as well (def complement).

It will return the complement sequence to a given DNA/RNA sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3040

def return_complement(
    i = dna_sequence?
  )
  return ::Bioroebe::NucleotideModule.complementary_strand(i)
end

#return_default_GFP_sequence(path_to_the_file = FILE_GFP_SEQUENCE) ⇒ Object

#

return_default_GFP_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 2959

def return_default_GFP_sequence(
    path_to_the_file = FILE_GFP_SEQUENCE
  )
  Fasta.new(path_to_the_file) { :be_quiet }.return_sequence
end

#return_dna_nucleotides ⇒ Object

#

return_dna_nucleotides

This method will return the Array holding A, T, C and G (the four DNA nucleotides).

#


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# File 'lib/bioroebe/shell/shell.rb', line 7553

def return_dna_nucleotides
  %w( A T C G )
end

#return_dna_sequence_as_sequence_object ⇒ Object Also known as: main_sequence?, dna_sequence_object?, sequence_object?, sequence?, seq_object?, sequence, seq_obj?, last_nucleotide_sequence?

#

return_dna_sequence_as_sequence_object

This method will always return the main “sequence object” in question, which is (almost always) a DNA sequence (dsDNA).

#


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# File 'lib/bioroebe/shell/shell.rb', line 830

def return_dna_sequence_as_sequence_object
  @internal_hash[:array_dna_sequences].last
end

#return_fasta_files_in_the_log_directory ⇒ Object

#

return_fasta_files_in_the_log_directory

#


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# File 'lib/bioroebe/shell/shell.rb', line 7574

def return_fasta_files_in_the_log_directory
  Dir[::Bioroebe.log_dir?+'*.fa*']
end

#return_pwd ⇒ Object Also known as: return_default_prompt

#

return_pwd

#


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# File 'lib/bioroebe/shell/shell.rb', line 5108

def return_pwd
  ("#{Dir.pwd}/").squeeze('/')
end

#return_random_aminoacid ⇒ Object

#

return_random_aminoacid

#


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# File 'lib/bioroebe/shell/shell.rb', line 2190

def return_random_aminoacid
  Bioroebe.return_random_aminoacid
end

#return_random_nucleotide ⇒ Object Also known as: add_nucleotide

#

return_random_nucleotide

Here we return a random nucleotide.

#


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# File 'lib/bioroebe/shell/shell.rb', line 995

def return_random_nucleotide
  return Bioroebe.return_random_nucleotide
end

#return_random_restriction_enzyme(be_verbose = false) ⇒ Object

#

return_random_restriction_enzyme

This method will return a random restriction enzyme, such as:

["EgeI", "GGCGCC 3"]
#


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# File 'lib/bioroebe/shell/shell.rb', line 9022

def return_random_restriction_enzyme(be_verbose = false)
  splitted = ::Bioroebe.restriction_enzymes.sample
  _ = splitted[1].split(' ')[0]
  if be_verbose
    erev 'Now adding restriction site `'+red(splitted[0])+
         '` (cuts at '+simp(_)+').'
  end
  return _
end

#return_reverse_dna_string ⇒ Object

#

return_reverse_dna_string

#


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# File 'lib/bioroebe/shell/shell.rb', line 5914

def return_reverse_dna_string
  complement_sequence?.reverse
end

#return_sequence_from_this_number(i = 1) ⇒ Object

#

return_sequence_from_this_number

#


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# File 'lib/bioroebe/shell/shell.rb', line 2707

def return_sequence_from_this_number(i = 1)
  case i.to_i
  when 1
    seq1?
  when 2
    seq2?
  when 3
    seq3?
  when 4
    seq4?
  when 5
    seq5?
  when 6
    seq6?
  end
end

#reverse_complement(i = sequence? ) ⇒ Object

#

reverse_complement (reverse complement tag)

Reverse-Complement a given sequence at hand. In other words, if given a sequence of DNA or RNA, we will first build the complement to that DNA sequence, and then reverse that complement.

In the shell interface, you can test this like so:

assign AAATTT; reverse_complement
#


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# File 'lib/bioroebe/shell/shell.rb', line 6836

def reverse_complement(
    i = sequence?
  )
  i = sequence? if i.nil?
  if i.nil?
    report_that_a_string_must_be_assigned_first
    erev 'Example:'
    e
    e simp('  assign TTATTA')
    e
  else
    result = padding?+leading_five_prime+
             sfancy(
               return_complement(i.reverse)
             )+rev+
             trailing_three_prime
    result << ' ('+orange(i.size)+rev+' nucleotides)'
    erev result
  end
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/shell/shell.rb', line 11505

def run
  # if Bioroebe.is_on_roebe?
  #   # =================================================================== #
  #   # Load up support for FtpParadise, but only on roebe-systems.
  #   # As of Nov 2023 this has been disabled.
  #   # =================================================================== #
  #   begin
  #     require 'ftp_paradise'
  #   rescue LoadError; end
  # end
  setup_readline if use_readline? # This should come before we perform the startup actions.
  perform_startup_actions # Should come before we show the welcome message or call menu().
  show_welcome_message    # The welcome-message should come after the startup actions.
  menu(
    commandline_arguments?,
    :be_quiet_if_the_input_was_not_found
  )
  if runmode_is_commandline?
    # ===================================================================== #
    # Enter the main user-input loop here if we are working in
    # commandline-mode.
    # ===================================================================== #
    enter_the_main_loop
  end
end

#run_in_GUI_mode? ⇒ Boolean Also known as: run_as_GUI?, run_in_GUI_settings?, run_in_GUI_setting?

#

run_in_GUI_mode?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 10121

def run_in_GUI_mode?
  runmode? == :GUI
end

#run_nls_search ⇒ Object

#

Search the sequence for NLS.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4614

def run_nls_search
  if aminoacids?
    erev 'We will try to run a NLS search on '+simp(aminoacids?.to_s)+':'
    e
    erev "  #{sfancy(aminoacids?.to_s)}"
    e
    ARRAY_NLS_SEQUENCES.each {|sequence|
      if aminoacids?.include? sequence
        erev 'We found a result for -> '+swarn(sequence)
      else
        e sfancy(sequence)+' <- This NLS is not included.'
      end
    }
  else
    erev 'Please first assign an '+sfancy('aminoacid sequence')+
         ' such as by doing:'
    e
    erev '  set_aminoacids '+
         ::Bioroebe.colourize_aa('PAAKRVKLKKKKKKKKKRKKKPPKLKVKVKLKLKAA')
    e
  end
end

#run_sizeseq ⇒ Object

#

run_sizeseq

This method essentially does what the Emboss sizeseq is doing.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8427

def run_sizeseq
  last_fasta_entry?.do_sort_by_size
end

#run_sql_query(i, be_verbose = true, optional_append_this = '') ⇒ Object Also known as: sql_query, run_query, run_sql

#

run_sql_query

#


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# File 'lib/bioroebe/shell/shell.rb', line 7101

def run_sql_query(
    i,
    be_verbose           = true,
    optional_append_this = ''
  )
  ::Bioroebe.run_sql_query(i, be_verbose, optional_append_this)
end

#run_this_user_input ⇒ Object

#

menu (menu tag)

#

run_this_user_input()



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# File 'lib/bioroebe/shell/menu.rb', line 5359

def menu(
    i                                     = command_to_be_passed_to_the_menu?,
    report_if_we_did_not_find_the_command = true
  )
  # ======================================================================= #
  # === Handle special instructions given to the second arguments
  # ======================================================================= #
  case report_if_we_did_not_find_the_command
  # ======================================================================= #
  # === :dont_report
  # ======================================================================= #
  when :dont_report,
       :be_quiet,
       :be_quiet_if_the_input_was_not_found
    report_if_we_did_not_find_the_command = false
  end
  if i.is_a?(Array) and !i.empty?
    i.flatten.each {|entry|
      menu(entry, report_if_we_did_not_find_the_command)
    }
  else
    i = i.to_s.strip
    case i # (case tag, casetag, realcase tag)
    # ===================================================================== #
    # === bioroebe --sinatra
    #
    # This entry point starts the sinatra web-interface.
    # ===================================================================== #
    when /^-?-?sinatra2$/i,
         /^-?-?start(_|-| )?sinatra2$/i,
         /^-?-?sinatra$/i
      do_start_the_sinatra_interface
    # ===================================================================== #
    # === mkdir
    # ===================================================================== #
    when /^mkdir$/
      mkdir(f?)
    # ===================================================================== #
    # === no_colours
    # ===================================================================== #
    when 'nocol',
         'noco',
         /^-?-?no(_|-| )?colou?rs?$/,
         /^-?-?disable(_|-| )?colours$/,
         'dcolours'
      disable_colours
    # ===================================================================== #
    # === disable_colours_in_an_extended_manner
    # ===================================================================== #
    when /disable(_|-| )?colours(_|-| )?in(_|-| )?an(_|-| )?extended(_|-| )?manner$/
      disable_colours_in_an_extended_manner(:be_verbose)
    # ===================================================================== #
    # === uniprot
    #
    # This entry point allows the user to download data from uniprot
    # quickly, via the bioshell interface.
    #
    # Invocation examples:
    #
    #   uniprot 2BTS
    #   uniprot A2Z669
    #
    # ===================================================================== #
    when /^uniprot(_|-| )?fetch$/,
         /^uniprot$/i,
         /^unifetch$/i,
         /^fetch(_|-| )?data(_|-| )?from(_|-| )?uniprot$/
      result = uniprot_fetch(f)
      set_result(result)
    # ===================================================================== #
    # === dna_seq?
    # ===================================================================== #
    when 'dna_seq?',
         'dnaseq?',
         'seq?',
         'seqß',
         'dna?',
         'sequence?',
         'string?',
         'sq?',
         'data?',
         's?',
         'show2',
         'show?',
         'report?',
         'print',
         'output',
         /^show(_|-| )?string$/i,
         /^print(_|-| )?dna$/i,
         /^show(_|-| )?dna$/i,
         /^main(_|-| )?string$/i,
         /^show(_|-| )?dna(_|-| )?sequence$/i,
         /^showsequence$/i,
         /^showseq$/i,
         /^dna(_|-| )?string\??$/i,
         'mainstring?',
         'mstring?',
         'dnaß',
         'sdna',
         'normal',
         'DNA?'
      show_dna_sequence
    # ===================================================================== #
    # === Bioroebe.sequence
    # ===================================================================== #
    when 'Bioroebe.sequence?',
         'Bioroebe.seq?'
      e Bioroebe.sequence?
    # ===================================================================== #
    # === dna_sequence?
    # ===================================================================== #
    when /^dna_?sequence\?$/
      pp dna_sequence?
    # ===================================================================== #
    # === fasta?
    # ===================================================================== #
    when 'fasta?',
         /handle_?fasta/ # Feedback information from a local fasta file.
      handle_fasta(a?)
    # ===================================================================== #
    # === chop_to
    #
    # Usage example:
    #
    #   chop_to :ATG
    #
    # ===================================================================== #
    when /^chop_?to$/
      chop_to(a?)
    # ===================================================================== #
    # === chop
    # ===================================================================== #
    when 'chop'
      chop(a?)
    # ===================================================================== #
    # === choppity
    # ===================================================================== #
    when 'choppity',/chop_?codon/
      chop(3)
    # ===================================================================== #
    # === chop33
    # ===================================================================== #
    when /chop(\d+)/ # See: http://rubular.com/r/VWiUYgr5Xq
      chop($1.to_s)
    # ===================================================================== #
    # === default_colours_for_the_aminoacids
    # ===================================================================== #
    when /default(_|-| )?colours(_|-| )?for(_|-| )?the(_|-| )?aminoacids/
      e
      config?.default_colours_for_the_aminoacids.each_pair {|one_letter, colour_to_use|
        e '  '+one_letter+' '+
          ::Colours.send(colour_to_use.to_sym, colour_to_use)+
          rev
      }
      e
    # ===================================================================== #
    # === bioshell_log_dir?
    # ===================================================================== #
    when /bioshell(_|-| )?log(_|-| )?dir\??/i
      e
      e steelblue("  #{log_dir?}bioshell/")
      e
    # ===================================================================== #
    # === dna_to_aminoacids
    #
    # Usage example:
    #
    #   toAA ACGTACGTAGTCATCAGTCAGTA
    #
    # ===================================================================== #
    when /^dna_?to_?aminoacids$/,
         'translate_dna_into_aminoacid',
         'translatednaintoaminoacid',
         'trans',
         'transl',
         'trnas',
         'translateaminoacidintodna',
         'toprotein',
         'to_protein',
         'to_aminoacid',
         'to_aminoacids',
         'aa',
         'toproteins',
         'toaminoacids',
         /to(_|-| )?aa/i,
         'translate',
         'mega',
         'toprotei',
         'translate_aminoacids',
         'toprot',
         'toamin',
         'toamino'
      arguments = a?
      if arguments and arguments.is_a?(Array) and arguments.empty?
        arguments = dna_sequence_as_string?
      end
      show_all_deducible_aminoacid_sequences(arguments)
      if dna_seq?.empty? # This here is ok because the above method checks whether there was a DNA sequence assigned.
        return
      else
        e
        show_protein_composition(
          translate_dna_into_aminoacid(arguments)
        )
        if arguments.empty?
          arguments = dna_sequence?.dup unless a
        end
        ::Bioroebe::DnaToAminoacidSequence.new(arguments)
      end
    # ===================================================================== #
    # === set_dna_sequence
    #
    # Usage examples:
    #
    #   set_sequence /Depot/j/foobar.fasta
    #   set_sequence ACGTACGTACA
    #   set_sequence 555
    #
    # ===================================================================== #
    when 'set_dna_sequence',
         'setdnasequence',
         'setdna',
         'assign',
         'set_dna',
         'assign_sequence',
         'sequence',
         'seq',
         's',
         'asign',
         'set_seq',
         'setseq',
         'assing',
         'set',
         'assig',
         'set_string',
         'setstring',
         'ass',
         'setseq1',
         'setda',
         'read',
         /^assign(_|-| )?dna$/,
         /^assign(_|-| )?this(_|-| )?dna(_|-| )?sequence$/,
         /^set(_|-| )?sequence$/
      set_dna_sequence(a?, :be_verbose) # Always be verbose.
      show_sequence
    # ===================================================================== #
    # === to_mRNA
    # ===================================================================== #
    when /^to(_|-| )?mRNA$/i,
         'mrna',
         /convert_five_prime_dna_into_five_prime_mrna/i
      convert_five_prime_dna_into_five_prime_mrna
    # ===================================================================== #
    # === random
    # ===================================================================== #
    when 'random',
         'rand',
         'ran',
         'ra',
         'random?',
         'rand?',
         'generate',
         'randomseq',
         'ramdpm',
         'setrandom',
         'andom',
         'rando',
         'raond',
         'rnadom',
         'ranom',
         'ranomd',
         'create'
      random(f, remaining_arguments?) # Generate some DNA sequence.
      show_dna_sequence
    # ===================================================================== #
    # === random_dna
    # ===================================================================== #
    when 'random_dna',
         'generate_dna3','generate_dna_variable_composition',
         'generate_random_dna_sequence_with_variable_length_and_variable_composition',
         'generatedna3',
         'generatednavariablecomposition',
         'gdna3',
         'randomdna'
      result = generate_random_dna_sequence_with_variable_length_and_variable_composition
      e result # Display it.
      assign_sequence(result) # And assign it too.
    # ===================================================================== #
    # === is_a_aminoacid?
    #
    # To test this entry point, try:
    #
    #   is_a_aminoacid? Alanin  # => false
    #   is_a_aminoacid? Alanine # => true
    #
    # ===================================================================== #
    when 'is_a_aminoacid?','isaa?'
      pp ::Bioroebe.is_aminoacid?(f?)
    # ===================================================================== #
    # === piped
    # ===================================================================== #
    when 'piped',
         /^show_?codon_?piped_?sequence$/i,
         /^vertical(_|-| )?bar$/i,
         'as_pipe',
         /^codon(_|-| )?piped$/i
      show_codon_piped_sequence
    # ===================================================================== #
    # === pubmed_search
    #
    # Invocation example:
    #
    #   pubmed_search science[journal]+AND+breast+cancer+AND+2008[pdat]
    #
    # ===================================================================== #
    when /^pubmed(_|-| )?search/
      perform_a_pubmed_search(all_arguments?)
    # ===================================================================== #
    # === nohyphen
    #
    # This entry point removes all hyphens.
    #
    # Example:
    #
    #   nohyphen GCA-GCA-AGA-GGA-CTA-AAA-AAA-AAA-CTA-AAA-CTA-ATG-ATG-GCA-GCA-GCA-GCA-GCA
    #
    # ===================================================================== #
    when /nohyphen/
      erev a.join.delete('-')
    # ===================================================================== #
    # === random_aa
    # ===================================================================== #
    when 'random_aa',
         'randomaa',
         'set_random_aminoacids',
         'randomAA',
         'random_aminacids',
         'create_random_aminoacids',
         'random_aminoacids',
         'randomaminoacids'
      set_random_aminoacids
    # ===================================================================== #
    # === all_aminoacids?
    # ===================================================================== #
    when 'all_aminoacids?','display_all_aminoacids','displayallaminoacids',
         'shortnames?',
         'print_aa',
         'printaa',
         'daminoacids',
         'aminoacids_shortnames'
      display_all_aminoacids
    # ===================================================================== #
    # === report_n_start_codons
    #
    # This entry point will report how many start codons can be found
    # in the main Sequence.
    #
    # Invocation example:
    #
    #   report_n_start_codons
    #
    # ===================================================================== #
    when /^report(_|-| )?n(_|-| )?start(_|-| )?codons$/i
      report_n_start_codons
    # ===================================================================== #
    # === palindromes?
    # ===================================================================== #
    when 'palindromes?',
         'PalindromeFinder',
         'pali',
         'palindrome?',
         'pfinder',
         'palindromes'
      ::Bioroebe::PalindromeFinder.new(dna_string?)
    # ===================================================================== #
    # === is_palindrome?
    #
    # Usage examples:
    #
    #   is_palindrome? ATTA
    #   is_palindrome? ATAT
    #
    # ===================================================================== #
    when 'is_palindrome?',
         'ispalindrome?',
         'is_palindrome',
         'is_palindromic?',
         'is_pal?',
         'palindromic?',
         'palinomer?'
      is_palindrome?(f)
    # ===================================================================== #
    # === append
    # ===================================================================== #
    when 'append','<<','merge'
      append(a?) # Call it directly.
    # ===================================================================== #
    # === clear
    # ===================================================================== #
    when 'clear'
      clear(a?)
    # ===================================================================== #
    # === print_aa_table
    # ===================================================================== #
    when 'table_aa','tableaa','print_aa_table','printaatable',
         'molmassen','supertable','table?','maintable',
         'amino_acid_weight','aatable',
         'print_aminoacid_table',
         'patable',
         /^Aminoacids(_|-| )?Mass(_|-| )?Table$/i,
         /^aminoacids(_|-| )?weights\??$/i,
         /^aas(_|-| )?weights\??$/i
      print_aa_table
    # ===================================================================== #
    # === degenerate_primer
    #
    # Invocation example:
    #
    #   dprimer M-T-T-Y-Y-T-A-A-A-STOP
    #
    # ===================================================================== #
    when /^degenerate(_|-| )?primer$/i,
         'degenerate',
         'dprimer', # dprimer M-T-T-Y-Y-T-A-A-A-STOP
         'dprime',
         'dprim',/back_?to_?dna/
      a = aminoacid_sequence? if a.nil? or a.empty?
      dna_sequence = ConvertAminoacidToDNA.new(a?).dna_sequence?.delete('-') # bl $BIOROEBE/convert_aminoacid_to_dna.rb
      erev swarn('Note')+rev+': If you want to assign this DNA sequence to become the new'
      erev 'main sequence, then input:'
      e
      erev orange('  assign_this_dna_sequence')
      e
      @internal_hash[:misc_sequence] = dna_sequence 
    # ===================================================================== #
    # === show_codon_table
    #
    # This entry point can be used to show the (default) codon table,
    # aka the eukaryotic codon table.
    #
    # Usage examples:
    #
    #   ctable
    #   ctable 4
    #
    # ===================================================================== #
    when /^show(_|-)?codon(_|-)?table$/i,
         'codontable?',
         'codontable',
         'codontable2',
         'codon_table?',
         'ctable',
         'ctble',
         'table2',
         'ctable?',
         'alltables'
      show_codon_table(a?)
    # ===================================================================== #
    # === aa_to_dna
    #
    # Translate the aminoacids to the DNA sequence.
    #
    # Usage examples:
    #
    #   aa_to_dna MTTT
    #   aa_to_dna KLMRST
    #
    # ===================================================================== #
    when /^aa(-|_)?to(-|_)?dna$/i
      aa_to_dna(a?)
    # ===================================================================== #
    # === pubmed?
    # ===================================================================== #
    when 'pub',
         'pubmed',
         'pubmed?' # pubmed tag
      pubmed(f?)
    # ===================================================================== #
    # === open_my_files
    # ===================================================================== #
    when /^open(_|-)?my(_|-)?files$/i,
         /^my(_|-)?files$/i,
         'ofiles'
      open_my_files
    # ===================================================================== #
    # === set_codon_table
    # ===================================================================== #
    when 'set_codon_table',
         'setcodontable',
         'codon_table=',
         'ctable=',
         /^choose(_|-)?codon(_|-)?table$/i,
         'choosecodontable',
         'pick_codon_table',
         'codon_table',
         'setcodon',
         'set_codon'
      set_codon_table(f)
    # ===================================================================== #
    # === left_add
    #
    # This will add n nucleotides to the "left" end, aka the 5' end of
    # a DNA or RNA sequence.
    #
    # Invocation example:
    #
    #   left_add 10
    #   ladd 20
    #
    # ===================================================================== #
    when /left(_|-)?add/,
         'ladd'
      left_add(a?)
    # ===================================================================== #
    # === last_input?
    # ===================================================================== #
    when 'last_input?','input?','show_last_input','sli',
         'showlastinput'
      show_last_input
    # ===================================================================== #
    # === human_chromosome_22
    #
    # The human chromosome number 22.
    # ===================================================================== #
    when 'human_chromosome_22'
      _ = 'http://hgdownload.cse.ucsc.edu/goldenpath/hg19/chromosomes/chr22.fa.gz'
      e _
      download _
    # ===================================================================== #
    # === sendai
    #
    # The Sendai virus genome, a 15384 bp genome.
    # ===================================================================== #
    when 'sendai'
      e 'https://www.ncbi.nlm.nih.gov/nuccore/9627219'
    # ===================================================================== #
    # === set_start_codon
    # ===================================================================== #
    when 'set_start_codon',
         'setstartcodon',
         'start_codon=',
         'setinitcodon'
      set_start_codon(f)
    # ===================================================================== #
    # === ncbi_taxonomy?
    # ===================================================================== #
    when 'ncbi_taxonomy?'
      browse_to 'http://www.ncbi.nlm.nih.gov/taxonomy/'
    # ===================================================================== #
    # === itax
    # ===================================================================== #
    when 'itax','taxonomy',
         'tax'
      ::Bioroebe::Taxonomy.interactive :run_connected
    # ===================================================================== #
    # === show_remote_urls
    # ===================================================================== #
    when /^show(_|-)?remote(_|-)?urls$/i,
         'url',
         'taxonomy_urls?',
         'remote_url',
         'ncbi?',
         'sremote'
      Bioroebe.show_remote_urls_to_the_NCBI_taxonomy_webpage(f)
    # ===================================================================== #
    # === n_species?
    # ===================================================================== #
    when 'n_species?',
         'n_species',
         'nspecies?',
         'nspecies',
         /^report(_|-| )?n(_|-| )?species$/i
      ::Bioroebe::Taxonomy.report_n_species
    # ===================================================================== #
    # === home?
    # ===================================================================== #
    when /^home\??$/i
      report_where_the_home_directory_can_be_found
    # ===================================================================== #
    # === codon
    #
    # This entry point will quickly show the codon (the aminoacid
    # sequence) of the given input sequence.
    #
    # Usage example:
    #
    #   codon AAAGUCCAUAAA
    #
    # ===================================================================== #
    when 'codon'
      codon(a?)
    # ===================================================================== #
    # === to_rna
    # ===================================================================== #
    when '@rna',
         'to_rna',
         /^-?-?to_?RNA$/i,
         'rna',
         'dna2rna', # You can also use this like so: ATCGTTGC.to_rna
         'rna_translate',
         'rnatranslate',
         'rna?',
         'transcribe',
         'rawrna'
      show_rna_sequence(f)
    # ===================================================================== #
    # === automatically_rename_this_fasta_file
    #
    # This entry-point can be used to automatically rename a FASTA file.
    # ===================================================================== #
    when /^-?-?automatically(_|-)?rename(_|-)?this(_|-)?fasta(_|-)?file$/i,
         /^-?-?infer(_|-)?fasta$/i,
         /^-?-?ifasta$/i
      automatically_rename_this_fasta_file(a)
    # ===================================================================== #
    # === show_both_strands
    # ===================================================================== #
    when 'show_both_strands',
         'both','dual',
         'showbothstrands',
         /^-?-?show(_|-)?both(_|-)?dna(_|-)?strands$/i,
         'double',
         'show_double_strand',
         /^dsDNA$/i
      show_both_dna_strands
    # ===================================================================== #
    # === UAG?
    # ===================================================================== #
    when /^UAG\??$/i
      this_sequence = dna_string?
      use_this_start_codon = 'UAG'
      if this_sequence.include? 'U'
      else
        use_this_start_codon = 'TAG'
      end
      _ = search_sequence_for_open_reading_frames(
        this_sequence,
        :frame1, # use_which_frame
        use_this_start_codon
      )
      if _.empty?
        erev 'No substring '+i.to_s.delete('?')+' was found.'
      else
        show_nucleotide_sequence?.display(i) {{ colourize_this_subsequence: use_this_start_codon }}
      end
    # ===================================================================== #
    # === size?
    # ===================================================================== #
    when 'size?',
         'nuc?',
         'size',
         'nsizes',
         'nsize',
         'length?',
         'len?',
         'len',
         'report_length_of_the_dna_string',
         'sizeß',
         'n?'
      report_size_of(f?)
    # ===================================================================== #
    # === find_orfs
    # ===================================================================== #
    when 'find_orfs',
         /^find(_|-)?all(_|-)?orfs$/i,
         'forfs','forf'
      find_all_orfs
    # ===================================================================== #
    # === prepend_start
    # ===================================================================== #
    when 'pstart',
         'prepend_start',
         'appendstart',
         'start'
      add_to_start :start
    # ===================================================================== #
    # === fancy
    # ===================================================================== #
    when 'fancy'
      display_open_reading_frames
    # ===================================================================== #
    # === fetch
    #
    # This entry point allows the user to fetch a (remote) .pdb file.
    #
    # Invocation example:
    #
    #   fetch 2BTS
    #
    # ===================================================================== #
    when /^fetch(_|-)?from(_|-)?pdb$/,
         'fetch'
      fetch_from_pdb(f)
    # ===================================================================== #
    # === reverse_complement
    #
    # This entry point will build the "reverse complement" sequence
    # to a given DNA sequence at hand.
    # ===================================================================== #
    when /^reverse(_|-)?complement$/i,
         /^rev(_|-)?complement$/i,
         'rcomplement',
         'rcompl'
      reverse_complement(f)
    # ===================================================================== #
    # === P00995
    # ===================================================================== #
    when 'P00995'
      oib 'https://www.uniprot.org/uniprot/P00995'
      download_this_fasta_sequence 'https://www.uniprot.org/uniprot/P00995.fasta'
    # ===================================================================== #
    # === brenda
    # ===================================================================== #
    when /^brenda$/i
      open_in_browser('https://www.brenda-enzymes.org/')
    # ===================================================================== #
    # === expasy
    # ===================================================================== #
    when /^expasy$/i
      open_expasy(a?)
    # ===================================================================== #
    # === 9cutters
    # ===================================================================== #
    when '9cutter',
         '9cutters',
         '9-cutters',
         '9cut'
      show_restriction_enzymes '9'
    # ===================================================================== #
    # === code?
    # ===================================================================== #
    when 'code?','code','translate_aminoacids_into_dna'
      translate_aminoacids_into_dna(a?)
    # ===================================================================== #
    # === wormbase?
    # ===================================================================== #
    when 'wormbase?',
         'wormbase'
      e (_ = Bioroebe.try_to_pass_through_beautiful_url(_))
        open_in_browser _
    # ===================================================================== #
    # === promoters?
    # ===================================================================== #
    when /^promoters?\??$/,
         /^search_?for_?known_?promoters$/
      search_for_known_promoters
    # ===================================================================== #
    # === samino
    # ===================================================================== #
    when 't2','translate2','aminoacid??','shorten',
         /shorten_?aminoacid/,'samino',
         'saminoacid'
      shorten_aminoacid(a?)
    # ===================================================================== #
    # === frameshift
    # ===================================================================== #
    when 'frameshift','frame','shift','shifter','shifting',
         'perform_frameshift_action','performframeshiftaction',
         'fr','frame?'
      perform_frameshift_action(a?)
    # ===================================================================== #
    # === GPCR?
    # ===================================================================== #
    when 'GPCR?','gpcr?'
      _ = 'http://www.gpcr.org/7tm/'
      e simp(_)+rev
      set_xorg_buffer(_) if @configuration.additionally_set_xorg_buffer
    # ===================================================================== #
    # === generate_random_protein_sequence_with_variable_length_and_variable_composition'
    # ===================================================================== #
    when /^generate(_|-)?random(_|-)?protein(_|-)?sequence(_|-)?with(_|-)?variable(_|-)?length(_|-)?and(_|-)?variable(_|-)?composition$/
      generate_random_protein_sequence_with_variable_length_and_variable_composition
    # ===================================================================== #
    # === wobble?
    # ===================================================================== #
    when 'wobble',
         'wobble?'
      erev 'CAGUI, G->C(U) und U->A(G)sowie I->U,C,A, an der '\
           '5 Prime Position der tRNA.'
    # ===================================================================== #
    # === RNAfold2
    # ===================================================================== #
    when 'RNAfold2'
      esystem 'RNAfold -p --MEA < test.seq'
    # ===================================================================== #
    # === nucleotide_position?
    # ===================================================================== #
    when 'nucleotide_position?',
         'nucleotideposition?',
         'position?'
      show_position_for_the_main_sequence
    # ===================================================================== #
    # === find_gene
    # ===================================================================== #
    when 'find_gene',
         'findgene',
         'fgene',
         'genes?',
         'fingene'
      find_gene(a?)
    # ===================================================================== #
    # === to_talen
    # ===================================================================== #
    when /^to(-|_| )?talen$/,
         'talen',
         '2talen'
      to_talen(a?)
    # ===================================================================== #
    # === debug
    # ===================================================================== #
    when 'debug',
         'deb'
      f 'Toggling debug from '+sfancy(debug?.to_s)+' to: '
      do_toggle_debug_value
      e debug?
    # ===================================================================== #
    # === 2cutters
    # ===================================================================== #
    when '2cutter',
         '2cutters',
         '2-cutters',
         '2cut'
      show_restriction_enzymes '2'
    # ===================================================================== #
    # === 3cutters
    # ===================================================================== #
    when '3cutter',
         '3cutters',
         '3-cutters',
         '3cut'
      show_restriction_enzymes '3'
    # ===================================================================== #
    # === Handle input such as "658-660 =     CCA"
    # ===================================================================== #
    when /^(\d+)(\.\.|-)(\d+)\s*=\s*(.*)$/ # See: https://rubular.com/r/hDLHLND7cc
      _ = dna_sequence? # Keep a reference copy.
      start_position = $1.to_s.to_i # 11-12 = AA
      end_position   = $3.to_s.to_i
      new_sequence   = $4.to_s.strip
      old_sequence   = _[start_position-1, (end_position - start_position)+1]
      erev 'We will perform a match assignment at nucleotide position '+
           start_position.to_s+'-'+end_position.to_s+rev+
           '. The'
      erev 'old subsequence was: '+sfancy(old_sequence)+rev+
           ' - the new subsequence will be '+simp(new_sequence)
      new_sequence.delete!("'")
      _[start_position-1, (end_position - start_position)+1] = new_sequence
      set_dna_sequence(_)
    # ===================================================================== #
    # === dna_analyze
    # ===================================================================== #
    when /^dna(_|-)?analyze$/,
         'danalyze'
      analyze(a?) { :dna }
    # ===================================================================== #
    # === dash
    # ===================================================================== #
    when 'dash',
         'dashed',
         'spacer',
         /^splitted(_|-)?form$/
      show_sequence_in_splitted_form(f,'-')
    # ===================================================================== #
    # === leucine_zippers?
    # ===================================================================== #
    when 'leucine_zippers?','scan_for_leucine_zippers','leucine?',
         'leucinez','zippers','l?','leu?'
      scan_for_leucine_zippers(a?)
    # ===================================================================== #
    # === @aminoacids
    # ===================================================================== #
    when '@aminoacids'
      pp @internal_hash[:aminoacids]
    # ===================================================================== #
    # === open
    # ===================================================================== #
    when /^open$/i
      if f
        open(f)
      else
        open_my_files
      end
    # ===================================================================== #
    # === size_rna
    # ===================================================================== #
    when /^size(_|-)?rna$/i
      e @internal_hash[:rna].sequence.size.to_s
    # ===================================================================== #
    # === toggle_truncate
    # ===================================================================== #
    when /^toggle(_|-)?truncate$/i,
         /^truncate$/i
      toggle_truncate
    # ===================================================================== #
    # === 9mer
    # ===================================================================== #
    when '9mer',
         '9mer?'
      erev 'TTA|TCC|ACA'
      find_in_main_sequence('TTATCCACA')
      erev 'We found the 9mer n times: '+
            sfancy(string?.scan('TTATCCACA').size.to_s)
    # ===================================================================== #
    # === TAG?
    # ===================================================================== #
    when /^TAG\??$/i
      _ = search_sequence_for_open_reading_frames(
        i                    = string?,
        use_which_frame      = :frame1,
        use_this_start_codon = 'TAG'
      )
      if _.empty?
        erev 'No substring '+i.to_s.delete('?')+' was found.'
      else
        show_nucleotide_sequence?.display(i) {{ colourize_this_subsequence: use_this_start_codon }}
      end
    # ===================================================================== #
    # === inicodon?
    # ===================================================================== #
    when 'inicodon?',
         'startcodon?'
      erev ::Bioroebe.start_codon?
    # ===================================================================== #
    # === default_stop_codons?
    # ===================================================================== #
    when 'default_stop_codons?',
         'dstop?',
         'dna_codons?',
         'dna_codons',
         'dnacodons'
      pp ::Bioroebe.stop_codons? # This will be an Array.
    # ===================================================================== #
    # === discover_all_palindromes
    # ===================================================================== #
    when /^discover(_|-)?all(_|-)?palindromes$/i,
         /^dpalindromes$/i,
         'dpal'
      discover_all_palindromes(f)
    # ===================================================================== #
    # === dotplot
    # ===================================================================== #
    when /^dotplot$/i
      show_2D_dotplot(a?)
    # ===================================================================== #
    # === set_length
    # ===================================================================== #
    when /^set(_|-)?length$/i,
         /^set_?maxlength/,
         'length',
         'maxlength',
         'maxlen'
      set_default_length(a, :be_verbose)
    # ===================================================================== #
    # === replay
    # ===================================================================== #
    when 'replay',
         /^save(_|-)?history$/i
      replay(f)
    # ===================================================================== #
    # === raw_aa
    #
    # This entry point will simply display the raw aminoacid sequence,
    # translated from the main DNA sequence.
    # ===================================================================== #
    when /^raw(_|-)?aa$/i
      i = dna_sequence?
      sequence = ::Bioroebe::DnaToAminoacidSequence.new(i) { :be_quiet }.sequence
      e sequence
    # ===================================================================== #
    # === RNAfold3
    # ===================================================================== #
    when 'RNAfold3'
      esystem 'RNAfold -p < 5S.seq'
      esystem 'mountain.pl 5S_dp.ps | xmgrace -pipe'
      esystem 'relplot.pl 5S_ss.ps 5S_dp.ps > 5S_rss.ps'
    # ===================================================================== #
    # === mutate_position
    # ===================================================================== #
    when 'mutate_position','mutateposition','mposition','mpos'
      do_mutate_dna_sequence_at_this_nucleotide_position(a?) # mutate_position 5 C
    # ===================================================================== #
    # === include?
    # ===================================================================== #
    when 'include?',
         'inc?'
      include? f
    # ===================================================================== #
    # === cut
    # ===================================================================== #
    when /^cut$/i,
         'cutter'
      cut(f)
    # ===================================================================== #
    # === parse_gff
    # ===================================================================== #
    when /^-?-?parse(_|-)?gff$/i,
         'gff',
         'gff3',
         'gff?',
         'gff3?',
         /^-?-?scan(_|-)?gff$/i
      scan_or_parse_for_this_gff_file_or_any_gff_file(a?)
    # ===================================================================== #
    # === find
    # ===================================================================== #
    when /^try(_|-)?to(_|-)?find(_|-)?restriction(_|-)?enzymes(_|-)?for$/i,
         /scan(_|-)?for$/i,
         /look(_|-)?for$/i,
         'lfor',
         'find',
         'ind',
         'scan'
      try_to_find_restriction_enzymes_for(a?) # look_for
    # ===================================================================== #
    # === header?
    # ===================================================================== #
    when /^header\??$/i,
         /^headers\??$/i,
         /^show(_|-)?header(_|-)?of$/i
      show_header_of(a?)
    # ===================================================================== #
    # === uncolourize_this_aminoacid
    # ===================================================================== #
    when 'uncolourize',
         'uncolourize_this_aminoacid',
         'uncolourizethisaminoacid',
         'uncolaa',
         'uncola',
         '-colaa',
         'colremove',
         'ucola'
      uncolourize_this_aminoacid(f)
    # ===================================================================== #
    # === split
    # ===================================================================== #
    when 'split',
         'show_sequence_in_splitted_form'
      show_sequence_in_splitted_form(f)
    # ===================================================================== #
    # === namespace?
    # ===================================================================== #
    when 'namespace?'
      e namespace?
    # ===================================================================== #
    # === segments?
    # ===================================================================== #
    when 'segments?',
         'show_segments',
         'segments',
         'segmente'
      show_segments
    # ===================================================================== #
    # === to_rna2
    # ===================================================================== #
    when 'to_rna2'
      to_rna(f)
    # ===================================================================== #
    # === pathways?
    # ===================================================================== #
    when 'pathways?',
         'pathways',
         'pways',
         'pathway?',
         'pathway',
         'meta?',
         'path?',
         'show_all_pathways'
      show_all_pathways
    # ===================================================================== #
    # === aa_families?
    # ===================================================================== #
    when 'aa_families?',
         'aafamilies?',
         'aafamilies'
      pp ::Bioroebe.aa_families?
    # ===================================================================== #
    # === pfam?
    # ===================================================================== #
    when 'pfam?','pfam'
      e 'https://pfam.sanger.ac.uk/'
    # ===================================================================== #
    # === add
    # ===================================================================== #
    when 'add'
      add(a?)
    # ===================================================================== #
    # === set_padding
    # ===================================================================== #
    when /set_?padding/,
         'padding'
      set_padding(f, :be_verbose) # setpadding
    # ===================================================================== #
    # === ccaat?
    # ===================================================================== #
    when 'ccaat?',
         /^show(_|-)?ccaat(_|-)?sites$/,
         'ccaat',
         'ccaa'
      show_ccaat_sites
    # ===================================================================== #
    # === analyze
    # ===================================================================== #
    when 'analyze','ana?','analyze?'
      analyze(a?)
    # ===================================================================== #
    # === SSR?
    # ===================================================================== #
    when 'SSR?','ssr?','SSR','single_sequence_repeats'
      e generate_single_sequence_repeats
    # ===================================================================== #
    # === nucleotide?
    # ===================================================================== #
    when 'nucleotide?',
         'nucleotide',
         'ncbi_nucleotide_search_for'
      ncbi_nucleotide_search_for(a?)
    # ===================================================================== #
    # === three_letters_to_one_letter
    #
    # Usage example:
    #
    #   three_letters_to_one_letter THR
    #
    # ===================================================================== #
    when /^three(_|-)?letters(_|-)?to(_|-)?one(_|-)?letter$/i
      e three_letters_to_one_letter(a?)
    # ===================================================================== #
    # === rest_enzymes
    # ===================================================================== #
    when /^rest(_|-)?enzymes$/
      pp ::Bioroebe.show_restriction_enzymes
    # ===================================================================== #
    # === cutseq
    # ===================================================================== #
    when /^cutse(q|t)?$/i
      cutseq(a?)
    # ===================================================================== #
    # === first
    # ===================================================================== #
    when 'first',
         /^change(_|-)?first(_|-)?nucleotide(_|-)?to$/
      first(f)
    # ===================================================================== #
    # === pdf?
    # ===================================================================== #
    when 'pdf?','report_where_the_pdf_tutorial_can_be_found'
      report_where_the_pdf_tutorial_can_be_found
    # ===================================================================== #
    # === dmp?
    # ===================================================================== #
    when 'dmp?',
         /^show(_|-)?all(_|-)?dmp(_|-)?files$/,
         'dmp'
      show_all_dmp_files
    # ===================================================================== #
    # === codon?
    #
    # Invocation example in the BioShell:
    #
    #   codon? ATG
    #
    # ===================================================================== #
    when 'codon?',
         'kazusa_codon'
      show_codons_of_this_aminoacid_or_show_kazusa_codon(a?)
    # ===================================================================== #
    # === do_not_show_the_trailer
    # ===================================================================== #
    when /^-?-?do_?not_?show_?the_?trailer$/,
         /^-?-?no_?trailer$/
      do_not_show_the_trailer
    # ===================================================================== #
    # === edit
    # ===================================================================== #
    when /^edit$/i
      open_this_file_in_editor :bioshell
    # ===================================================================== #
    # === mpsa_source
    # ===================================================================== #
    when /^-?-?mpsa_?source/
      e '/opt/MPSA/mpsa/mpsa.bashrc'
    # ===================================================================== #
    # === assume?
    # ===================================================================== #
    when 'assume?',
         'assume',
         'assume_what_type_this_is'
      assume_what_type_this_is(a?) # assume ATTGGCCCATATTGGCC
    # ===================================================================== #
    # === bparse
    # ===================================================================== #
    when 'bparse',
         /^biolang(_|-)?parser$/
      BiolangParser.new # bl $BIOROEBE/biolang_parser.rb
    # ===================================================================== #
    # === set_prompt
    # ===================================================================== #
    when /^set(_|-)?prompt$/,
         'prompt',
         'setpwd'
      set_prompt(f)
    # ===================================================================== #
    # === no_prompt
    # ===================================================================== #
    when /^no(_|-)?prompt$/i
      set_prompt :empty
    # ===================================================================== #
    # === pyranose 2-oxidase
    # ===================================================================== #
    when /^pyranose(-|_)?2(-|_)?oxidase$/i
      e
      erev 'https://www.ncbi.nlm.nih.gov/nuccore/XM_008046051.1'
      e
    # ===================================================================== #
    # === disulfide?
    #
    # This entry point can be used to show disulfide positions in the
    # given sequence.
    # ===================================================================== #
    when /^-?-?disulfide\??$/i,
         /^-?-?show(_|-)?disulfides$/i
      show_disulfides
    # ===================================================================== #
    # === colourize_this_aminoacid
    # ===================================================================== #
    when 'colourize',
         /^colourize(_|-)?this(_|-)?aminoacid$/,
         'colaa',
         'cola',
         'colAA',
         'colourize_aminoacid'
      colourize_this_aminoacid(f)
    # ===================================================================== #
    # === frame2
    # ===================================================================== #
    when 'frame2',
         'f2'
      showorf(dna_sequence?, :frame2)
    # ===================================================================== #
    # === frame3
    # ===================================================================== #
    when 'frame3',
         'f3'
      showorf(dna_sequence?, :frame3)
    # ===================================================================== #
    # === mutate_aminoacid_position
    # ===================================================================== #
    when /^mutate(_|-)?aminoacid(_|-)?position$/
      mutate_aminoacid_position(a?)
    # ===================================================================== #
    # === interactive_colour_menu
    # ===================================================================== #
    when /^interactive(_|-)?colour(_|-)?menu$/,
         'icolours'
      interactive_colour_menu
    # ===================================================================== #
    # === aligned
    # ===================================================================== #
    when 'aligned',
         'aligned?',
         'beauty',
         'beautified', # We show the DNA sequence correctly aligned.
         'formatted',
         'padded',
         'beaut',
         'falign',
         'blocked',
         'block',
         /^show(_|-)?this(_|-)?sequence(_|-)?padded$/i
      show_this_sequence_padded(a?)
    # ===================================================================== #
    # === all_arguments
    # ===================================================================== #
    when /^arguments\??$/i
      pp all_arguments?
    # ===================================================================== #
    # === do
    #
    # do_action() as name is better than do(), in my opinion.
    # ===================================================================== #
    when 'do',
         /^do(_|-)?action$/i
      do_action(a?)
    # ===================================================================== #
    # === glutathione
    # ===================================================================== #
    when 'glutathione','glutathion'
      set_aminoacids('GCG')
    # ===================================================================== #
    # === relion_tags
    # ===================================================================== #
    when /^relion(_|-)?tags$/,
         'relion_tags?'
      e
      erev '_rlnImageName' 
      erev '_rlnCoordinateX' 
      erev '_rlnCoordinateY' 
      erev '_rlnMicrographName'
      erev '_rlnImageName'
      erev '_rlnDefocusU'
      erev '_rlnDefocusV'
      erev '_rlnDefocusAngle'
      erev '_rlnVoltage'
      erev '_rlnAmplitudeContrast'
      erev '_rlnSphericalAberration'
      e
    # ===================================================================== #
    # === project_base_dir
    # ===================================================================== #
    when /^project(_|-)?base(_|-)?dir$/i,
         'pdir',
         /^PROJECT(_|-)?BASE(_|-)?DIRECTORY$/i
      e Bioroebe.project_base_directory?
    # ===================================================================== #
    # === set_search
    # ===================================================================== #
    when /^set(_|-)?search$/i,
         /^set(_|-)?sequence$/i,
         /^set(_|-)?search(_|-)?string$/i,
         /^set(_|-)?search(_|-)?sequence$/i
      set_search_for(a?)
    # ===================================================================== #
    # === balanced
    # ===================================================================== #
    when /^create(_|-)?balanced(_|-)?composition$/i,
         'balanced'
      set_dna_string(
        create_balanced_composition(a?)
      )
    # ===================================================================== #
    # === show_local_sequences
    #
    # This entry point shows all local FASTA sequences - typically via
    # .fa or .fasta files.
    # ===================================================================== #
    when 'local_sequences?',
         'show_local_sequences',
         'showlocalsequences',
         'localfasta',
         'sequences?',
         'local?',
         'fastasequences?',
         'show_fasta_files',
         'localfasta?',
         'lfasta',
         /fasta(_|-)?files\??/
      show_local_sequences
      show_hint_how_to_use_the_local_sequences
    # ===================================================================== #
    # === compact_file
    # ===================================================================== #
    when /^compact(_|-)?file$/i,
         'compact',
         'cfile',
         'compacter'
      compact_file(f)
    # ===================================================================== #
    # === peroxisome_pts2
    # ===================================================================== #
    when 'peroxisome_pts2'
      erev 'H₂N-----Arg-Leu-X5-His-Leu-'
    # ===================================================================== #
    # === dna_translate
    # ===================================================================== #
    when /^dna(_|-)?translate/
      dna_translate(all_arguments?)
    # ===================================================================== #
    # === 1igt.pdb
    # ===================================================================== #
    when '1igt.pdb'
      erev 'https://www.rcsb.org/pdb/results/results.do?tabtoshow=Current&qrid=366A3EE'
    # ===================================================================== #
    # === MG1655
    # ===================================================================== #
    when 'MG1655'
      e
      efancy '  https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP032667.1'
      e
    # ===================================================================== #
    # === @configuration
    # ===================================================================== #
    when '@configuration'
      pp @configuration
    # ===================================================================== #
    # === colours?
    # ===================================================================== #
    when 'colours?','ucolours?','ucolours',
         /^will(_|-)?we(_|-)?use(_|-)?colours\??$/i
      will_we_use_colours?
    # ===================================================================== #
    # === @use_working_directory_as_prompt
    # ===================================================================== #
    when '@use_working_directory_as_prompt'
      pp @internal_hash[:use_working_directory_as_prompt]
    # ===================================================================== #
    # === uniprot?
    # ===================================================================== #
    when 'uniprot?',
         /^open(_|-)?in(_|-)?uniprot$/,
         'prot'
      open_in_uniprot(f)
    # ===================================================================== #
    # === HU?
    # ===================================================================== #
    when 'HU?',
         'heat-unstable',
         'heat-unstable-protein'
      erev 'heat-unstable protein in E. coli.'
      erev 'Encoded by hupA and hupB gene - see these links:'
      erev 'hupA:'
      erev '  '+NCBI_GENE+'948499'
      erev '  https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.3?report=fasta&from=4200281&to=4200553'
      erev 'hupB:'
      erev '  '+NCBI_GENE+'949095'
      erev '  https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.3?report=fasta&from=461451&to=461723'
    # ===================================================================== #
    # === snuc
    #
    # Invocation example:
    #
    #   snuc lady slipper orchid
    #
    # ===================================================================== #
    when /^search(_|-)?for(_|-)?nucleotide(_|-)?sequence/i,
         'snuc'
      search_for_nucleotide_sequence(a?) # Delegate into: http://www.ncbi.nlm.nih.gov/nucgss?term=G
    # ===================================================================== #
    # === fasta_header?
    # ===================================================================== #
    when /^show(_|-)?fasta(_|-)?headers$/i,
         'sfasta',
         /^fasta(_|-)?header\??/i,
         'showfasta',
         'fheader'
      show_fasta_headers(f)
    # ===================================================================== #
    # === copyright?
    # ===================================================================== #
    when /^copyright\??$/i
      show_copyright_clause
    # ===================================================================== #
    # === pBR322?
    # ===================================================================== #
    when /pBR322\??/
      e
      erev '  https://www.ncbi.nlm.nih.gov/nuccore/208958?report=fasta' # The pBR322 sequence.
      e
    # ===================================================================== #
    # === ARRAY_WITH_COMPLETIONS
    # ===================================================================== #
    when /^ARRAY(_|-)?WITH(_|-)?COMPLETIONS$/i
      pp ARRAY_WITH_COMPLETIONS
    # ===================================================================== #
    # === @array_these_sequences_were_chopped_away
    #
    # This entry point is mostly used for debugging-purposes.
    # ===================================================================== #
    when '@array_these_sequences_were_chopped_away',
         'chopped?'
      pp @internal_hash[:array_these_sequences_were_chopped_away]
    # ===================================================================== #
    # === array_colourize_this_aminoacid
    # ===================================================================== #
    when 'array_colourize_this_aminoacid'
      pp ::Bioroebe.array_colourize_this_aminoacid
    # ===================================================================== #
    # === @array_sequences
    # ===================================================================== #
    when '@array_sequences'
      pp array_sequences?
    # ===================================================================== #
    # === identical?
    # ===================================================================== #
    when 'identical?',
         'identical',
         'same',
         'same_content?',
         'similar?',
         'compare_two_files',
         'comparetwofiles'
      compare_two_files(f, second_argument)
    # ===================================================================== #
    # === locus?
    # ===================================================================== #
    when 'locus?'
      e @internal_hash[:locus]
    # ===================================================================== #
    # === molmass?
    # ===================================================================== #
    when 'mass?',
         'molecularmass?',
         'molmass?',
         'mmass',
         /^molecular(_|-)?mass(_|-)?of(_|-)?amino(_|-)?acids(_|-)?in(_|-)?the(_|-)?sequence$/i
      molecular_mass_of_amino_acids_in_the_sequence(f)
    # ===================================================================== #
    # === +
    #
    # Show the positively charged aminoacids.
    # ===================================================================== #
    when '+',
         'show_the_positively_charged_aminoacids'
      show_the_positively_charged_aminoacids
    # ===================================================================== #
    # === insulin?
    # ===================================================================== #
    when 'insulin?'
      show_insulin_entries_at_NCBI
    # ===================================================================== #
    # === list
    # ===================================================================== #
    when 'list'
      list(a?)
    # ===================================================================== #
    # === configdir?
    # ===================================================================== #
    when 'configdir?',
         /^show(_|-)?config(_|-)?dir$/i
      show_config_dir
    # ===================================================================== #
    # === show_nucleotides_table
    # ===================================================================== #
    when 'nucleotides?','nucleotide_table','nucleotidetable',
         'nucleotide_table?','nucleotidetable?','stable',
         'show_nucleotides_table','shownucleotidestable',
         'nucleotides_table?'
      show_nucleotides_table
    # ===================================================================== #
    # === print_table
    # ===================================================================== #
    when 'print_table','table','aa?','aminoacid_information',
         'print_aminoacid_information_table','aainfo',
         'aminosäuren','aminoacids','ptable','shortcuts?',
         'ainfo?','aainfo?','printtable','aa_table',
         'aminoacidstable?','aatable?'
      print_aminoacid_information_table
    # ===================================================================== #
    # === assigned?
    # ===================================================================== #
    when /assigned\??/,
         /is(_|-)?any(_|-)?nucleotide(_|-)?assigned\??/
      if is_any_nucleotide_assigned?
        erev 'A nucleotide sequence is assigned.'
      else
        erev 'No nucleotide sequence is assigned.'
      end
    # ===================================================================== #
    # === set_jumper_dir
    # ===================================================================== #
    when /set_?jumper_?dir/,'set_jumper','setjumper','sjumper'
        set_jumper_directory(f)
    # ===================================================================== #
    # === extract_sequence
    # ===================================================================== #
    when /extract_?sequence/,'extract','ext'
      extract_sequence(a?)
    # ===================================================================== #
    # === no_newlines
    # ===================================================================== #
    when /no_?newlines/
      no_newlines(a?)
    # ===================================================================== #
    # === run_sql_query
    # ===================================================================== #
    when 'run_sql_query','runsqlquery' # Input a sql command directly.
      run_sql_query(f)
    # ===================================================================== #
    # === Restriction enzymes
    #
    # Usage example for rest:
    #   rest AAAAAAAAGGCGCCCTGACCATCTAGAAAAA
    # ===================================================================== #
    when 'Bioroebe.restriction_enzymes?','all_restriction_enzymes',
         'allrestrictionenzymes'
      pp ::Bioroebe.restriction_enzymes?
    # ===================================================================== #
    # === search
    # ===================================================================== #
    when 'search','run',/start_?search/
      start_search
    # ===================================================================== #
    # === URLs?
    # ===================================================================== #
    when 'URLs?','URL?','URLS?',/show_?useful_?URLs/
      show_useful_URLs
    # ===================================================================== #
    # === NM_021964.1
    # ===================================================================== #
    when 'NM_021964.1','NM_021964' # This should one day be replaced with a NCBI-query system.
      e 'https://www.ncbi.nlm.nih.gov/nuccore/NM_021964.1'
      e 'https://www.ncbi.nlm.nih.gov/nuccore/NM_021964' # ← This is the updated variant.
    # ===================================================================== #
    # === first_orf?
    # ===================================================================== #
    when /first_?orf\??/,/show_?first_?orf/,'1storf','1st_ORF','1stORF'
      show_first_orf
    # ===================================================================== #
    # === emicroscopy
    # ===================================================================== #
    when 'emicroscopy'
      e 'This has not been ported yet - stay tuned.'
    # ===================================================================== #
    # === 4cutters
    # ===================================================================== #
    when '4cutter','4cutters','4-cutters','4cut'
      show_restriction_enzymes '4'
    # ===================================================================== #
    # === 5cutters
    # ===================================================================== #
    when '5cutter','5cutters','5-cutters','5cut'
      show_restriction_enzymes '5'
    # ===================================================================== #
    # === 6cutters
    # ===================================================================== #
    when '6cutter','6cutters','6-cutters','6cut'
      show_restriction_enzymes '6'
    # ===================================================================== #
    # === 7cutters
    # ===================================================================== #
    when '7cutter','7cutters','7-cutters','7cut'
      show_restriction_enzymes '7'
    # ===================================================================== #
    # === 8cutters
    # ===================================================================== #
    when '8cutter','8cutters','8-cutters','8cut'
      show_restriction_enzymes '8'
    # ===================================================================== #
    # === rawseq
    # ===================================================================== #
    when /rawseq\??/,
         'rawstring',
         'rawstring?',
         /dna_?sequence\??/,
         'fullseq',
         'realseq'
      e string? 
    # ===================================================================== #
    # === mutate
    # ===================================================================== #
    when 'mutate',
         'mutate_dna_sequence',
         'mutatednasequence'
      mutate_dna_sequence(a?)
    # ===================================================================== #
    # === setseq2
    # ===================================================================== #
    when /setseq2/, /seq2[^\?]/
      set_sequence_2(a?)
    # ===================================================================== #
    # === setseq3
    # ===================================================================== #
    when /setseq3/, /seq3[^\?]/
      set_sequence_3(a?)
    # ===================================================================== #
    # === setseq4
    # ===================================================================== #
    when /setseq4/, /seq4[^\?]/
      set_sequence_4(a?)
    # ===================================================================== #
    # === setseq5
    # ===================================================================== #
    when /setseq5/, /seq5[^\?]/
      set_sequence_5(a?)
    # ===================================================================== #
    # === setseq6
    # ===================================================================== #
    when /setseq6/, /seq6[^\?]/
      set_sequence_6(a?)
    # ===================================================================== #
    # === date
    # ===================================================================== #
    when 'date','show_date','showdate','sdate'
      show_date
    # ===================================================================== #
    # === colour_scheme_demo
    # ===================================================================== #
    when 'colour_scheme_demo','colourschemedemo','colour_tests',
         'colourtests','colourdemo'
      colour_scheme_demo
    # ===================================================================== #
    # === colour_scheme_for_aa
    # ===================================================================== #
    when 'colour_scheme_for_aa','colourschemeforaa',
         'colour_scheme_for_aminoacids','colour_scheme2',
         'caa','scheme_aa'
      colour_scheme_for_aminoacids(a?)
    # ===================================================================== #
    # === n_uracil?
    # ===================================================================== #
    when 'n_uracil?',
         'n_uracil',
         'nuracil',
         'nuracil?'
      n_uracil?
    # ===================================================================== #
    # === sixpack
    # ===================================================================== #
    when 'sixpack',
         '6pack',
         'show_sixpack_alignment','showsixpackalignment'
      show_sixpack_alignment(a?)
    # ===================================================================== #
    # === compseq
    #
    # This entry point is a wrapper over "compare sequence" aka compseq.
    # ===================================================================== #
    when 'compseq',
         'compseq?',
         /^compare(_|-)?the(_|-)?sequence$/i,
         'analyze_the_sequence',
         'csequ',
         'cseq',
         'compsqe',
         /^frequency(_|-)?analyzer$/i,
         'emboss',
         /^emboss(_|-)?compseq$/i,
         'dinucleotides',
         /^nucleotide(_|-)?frequency$/i
      compseq(a?) # bl compseq
    # ===================================================================== #
    # === show
    # ===================================================================== #
    when 'show',
         /^do(_|-)?show$/i
      show(a?)
    # ===================================================================== #
    # === generate_palindrome
    # ===================================================================== #
    when /^generate(_|-)?palindrome$/i,
         'palindrome',
         'palindrom',
         'pal',
         'pdrome'
      generate_palindrome(a?)
    # ===================================================================== #
    # === bioroebe --tk1                                           (tk tag)
    # ===================================================================== #
    when /^-?-?tk1$/i
      require 'bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb'
      Bioroebe::GUI::Tk::AminoacidComposition.new(ARGV)
    # ===================================================================== #
    # === bioroebe --tk2
    #
    # Invocation example:
    #
    #   bioroebe --tk-three-to-one
    #
    # ===================================================================== #
    when /^-?-?tk2$/i,
         /^-?-?tk(_|-| )?three(_|-| )?to(_|-| )?one$/i
      tk_start_three_to_one
    # ===================================================================== #
    # === bioroebe --tk3
    #
    # Invocation example:
    #
    #   bioroebe --tk3
    #
    # ===================================================================== #
    when /^-?-?tk3$/i
      require 'bioroebe/gui/tk/hamming_distance/hamming_distance.rb'
      Bioroebe::GUI::Tk::HammingDistance.new(ARGV)
    # ===================================================================== #
    # === start_and_stop?
    # ===================================================================== #
    when /^start_?and_?stop\??/
      report_colourized_sequence(:start_and_stop_codon)
    # ===================================================================== #
    # === start_and_stop
    # ===================================================================== #
    when /^start(_|-)?and(_|-)?stop$/i,
         '1+2',
         /^start(_|-)?stop$/i,
         'stopandstart',
         'yin_yang',
         '+-'
      show_start_and_stop_codons
    # ===================================================================== #
    # === stop_extended?
    # ===================================================================== #
    when 'stop_extended?'
      _ = main_sequence?
      stop_codons?.each {|this_stop_codon|
        _splitted = _.split(/#{this_stop_codon}/).each {|line|
          erev line+orange(this_stop_codon)+rev
        }
      }
      pp _splitted
    # ===================================================================== #
    # === rf "Horseradish Peroxidase"
    # ===================================================================== #
    when /^Horseradish(-|_)Peroxidase$/i
      show_resources_about_the_horseradish_peroxidase
    # ===================================================================== #
    # === mimivirus?
    # ===================================================================== #
    when /^mimivirus\??$/,'mimi'
      e 'Accession number is: '+
         sfancy('NC_014649')
    # ===================================================================== #
    # === user_input?
    #
    # This entry point is mostly used for debugging purposes.
    # ===================================================================== #
    when /^user(_|-)?input\??$/i
      pp @internal_hash[:user_input]
    # ===================================================================== #
    # === nls?
    # ===================================================================== #
    when 'nls?',
         'show_known_nls_sequences',
         'showknownnlssequences'
      show_known_nls_sequences
    # ===================================================================== #
    # === reste?
    # ===================================================================== #
    when 'reste?','show_reste','showreste','sreste'
      show_reste
    # ===================================================================== #
    # === test_colour_scheme
    # ===================================================================== #
    when /^test(_|-)?colour(_|-)?scheme$/i,
         'test_random_scheme'
      _ = random_dna_sequence
      colour_scheme_for_nucleotides(_)
    # ===================================================================== #
    # === compare_two_strings_as_alignment
    # ===================================================================== #
    when /compare_?two_?strings_?as_?alignment/i,'sstring','scompare',
         'sscompare','compare_two_strings','compare',
         /string_?compare/
      compare_two_strings_as_alignment(
        first_argument, second_argument
      ) # string_compare
    # ===================================================================== #
    # === left_chop
    #
    # This entry point allows the user to perform a so-called
    # "left-chop operation", aka to trim away nucleotides
    # that are on the left hand side of the sequence.
    # ===================================================================== #
    when /left(_|-)?chop$/,
         /left(_|-)?remove$/,
         /chop(_|-)?first$/,
         'chop5',
         'lchop'
      left_chop(a?)
    # ===================================================================== #
    # === translate_aminoacid
    #
    # Usage example:
    #
    #   translate kkrnn
    #
    # ===================================================================== #
    when /translate(_|-| )?aminoacid/i,
         'transaa',
         'translate_aa',
         'aminosäuren2',
         'translateaa',
         'trans2'
      translate_aminoacid(a?)
    # ===================================================================== #
    # === chi_sequence?
    # ===================================================================== #
    when 'chi_sequence?','chisequence?','chi?'
      e 'The chi sequence goes: '+simp('GCTGGTGG')
    # ===================================================================== #
    # === ncbi
    # ===================================================================== #
    when 'ncbi' # ncbi arabidopsis thaliana CDKs
      open_this_ncbi_page(a?)
    # ===================================================================== #
    # === pcolour
    # ===================================================================== #
    when 'interactively_pick_colour',
         'pick_colour',
         'pickcolour',
         'pcolour',
         'pcolor',
         'pcol'
      interactively_pick_colour
    # ===================================================================== #
    # === bioroebe --gtk1
    #
    # This is for alignment.rb
    # ===================================================================== #
    when /^-?-?gtk1$/i
      require 'bioroebe/gui/gtk3/alignment/alignment.rb'
      Bioroebe::GUI::Gtk::Alignment.run
    # ===================================================================== #
    # === bioroebe --gtk2
    #
    # This is for aminoacid_composition.rb
    # ===================================================================== #
    when /^-?-?gtk2$/i
      require 'bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb'
      Bioroebe::GUI::Gtk::AminoacidComposition.run
    # ===================================================================== #
    # === bioroebe --gtk3
    #
    # This is for anti_sense_strand.rb
    # ===================================================================== #
    when /^-?-?gtk3$/i
      require 'bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb'
      Bioroebe::GUI::Gtk::AntiSenseStrand.run
    # ===================================================================== #
    # === bioroebe --gtk4
    #
    # This is for blosum_matrix_viewer.rb
    # ===================================================================== #
    when /^-?-?gtk4$/i
      require 'bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb'
      Bioroebe::GUI::Gtk::BlosumMatrixViewer.run
    # ===================================================================== #
    # === bioroebe --gtk5
    #
    # This is for calculate_cell_numbers_of_bacteria.rb
    # ===================================================================== #
    when /^-?-?gtk5$/i
      require 'bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb'
      Bioroebe::GUI::Gtk::CalculateCellNumbersOfBacteria.run
    # ===================================================================== #
    # === bioroebe --gtk6
    #
    # This is for dna_to_aminoacid_widget.rb
    # ===================================================================== #
    when /^-?-?gtk6$/i
      require 'bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
      Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run
    # ===================================================================== #
    # === bioroebe --gtk7
    #
    # This is for dna_to_reverse_complement_widget.rb
    # ===================================================================== #
    when /^-?-?gtk7$/i
      require 'bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb'
      Bioroebe::GUI::Gtk::DnaToReverseComplementWidget.run
    # ===================================================================== #
    # === bioroebe --gtk8
    #
    # This is for fasta_table_widget.rb
    # ===================================================================== #
    when /^-?-?gtk8$/i
      require 'bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb'
      Bioroebe::GUI::Gtk::FastaTableWidget.run
    # ===================================================================== #
    # === bioroebe --gtk9
    #
    # This is for format_converter.rb
    # ===================================================================== #
    when /^-?-?gtk9$/i
      require 'bioroebe/gui/gtk3/format_converter/format_converter.rb'
      Bioroebe::GUI::Gtk::FormatConverter.run
    # ===================================================================== #
    # === bioroebe --gtk10
    #
    # This is for gene.rb
    # ===================================================================== #
    when /^-?-?gtk10$/i
      require 'bioroebe/gui/gtk3/gene/gene.rb'
      Bioroebe::GUI::Gtk::Gene.run
    # ===================================================================== #
    # === bioroebe --gtk11
    #
    # This is for hamming_distance.rb.
    # ===================================================================== #
    when /^-?-?gtk11$/i
      require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
      Bioroebe::GUI::Gtk::HammingDistance.run
    # ===================================================================== #
    # === bioroebe --gtk12
    #
    # This is for levensthein_distance.rb.
    # ===================================================================== #
    when /^-?-?gtk12$/i,
         /^-?-?gtk(_|-| )?levensthein$/i # bioroebe --gtk-levensthein
      require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
      Bioroebe::GUI::Gtk::LevenstheinDistance.run
    # ===================================================================== #
    # === bioroebe --gtk13
    #
    # This is for notebook.rb.
    # ===================================================================== #
    when /^-?-?gtk13$/i
      require 'bioroebe/gui/gtk3/controller/controller.rb'
      Bioroebe::GUI::Gtk::Controller.run
    # ===================================================================== #
    # === bioroebe --gtk14
    #
    # This is for nucleotide_analyser.rb.
    # ===================================================================== #
    when /^-?-?gtk14$/i
      require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
      Bioroebe::GUI::Gtk::NucleotideAnalyser.run
    # ===================================================================== #
    # === bioroebe --gtk15
    #
    # This is for parse_pdb_file.rb.
    # ===================================================================== #
    when /^-?-?gtk15$/i
      require 'bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb'
      Bioroebe::GUI::Gtk::ParsePdbFile.run
    # ===================================================================== #
    # === bioroebe --gtk16
    #
    # This is for primer_design_widget.
    # ===================================================================== #
    when /^-?-?gtk16$/i,
         /^-?-?primer(_|-| )?design$/i # bioroebe --primer-design
      require 'bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb'
      Bioroebe::GUI::Gtk::PrimerDesignWidget.run
    # ===================================================================== #
    # === bioroebe --gtk17
    #
    # This is for protein_to_DNA.
    # ===================================================================== #
    when /^-?-?gtk17$/i
      require 'bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb'
      Bioroebe::GUI::Gtk::ProteinToDNA.run
    # ===================================================================== #
    # === bioroebe --gtk18
    #
    # This is for random_sequence.
    # ===================================================================== #
    when /^-?-?gtk18$/i
      require 'bioroebe/gui/gtk3/random_sequence/random_sequence.rb'
      Bioroebe::GUI::Gtk::RandomSequence.run
    # ===================================================================== #
    # === bioroebe --gtk19
    #
    # This is for restriction_enzymes.
    # ===================================================================== #
    when /^-?-?gtk19$/i
      require 'bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb'
      Bioroebe::GUI::Gtk::RestrictionEnzymes.run
    # ===================================================================== #
    # === bioroebe --gtk20
    #
    # This is for show_codon_table.
    # ===================================================================== #
    when /^-?-?gtk20$/i
      require 'bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb'
      Bioroebe::GUI::Gtk::ShowCodonTable.run
    # ===================================================================== #
    # === at_content?
    #
    # Usage example:
    #
    #   at_content? AGTACGTACGTCAGTCA
    #
    # ===================================================================== #
    when /^at_?content\??$/i,
         'at?',
         'calc_at_content',
         'calcatcontent'
      calculcate_at_content(a?)
    # ===================================================================== #
    # === ll
    #
    # This is the general entry point for listing the content in the
    # current working directory.
    # ===================================================================== #
    when 'll',
         'ls',
         'l',
         'sdc',
         'lll',
         'llll',
         /^show(_|-)?file(_|-)?listing$/
      show_file_listing
    # ===================================================================== #
    # === remove
    #
    # This entry point can be used to remove a subsequence from the
    # 5' end (the "left" end).
    #
    # Invocation example:
    #
    #   remove 3
    #
    # ===================================================================== #
    when 'remove',
         'delete',
         'del',
         'rm'
      remove(a?)
    # ===================================================================== #
    # === oligo_two
    # ===================================================================== #
    when 'oligo_two',
         'oligo_length_two',
         'oligolengthtwo',
         'two',
         'oligonucleotide_frequency'
      show_oligo_length_two
    # ===================================================================== #
    # === efetch
    # ===================================================================== #
    when /^efetch$/
      efetch(a?)
    # ===================================================================== #
    # === Handle aminoacid sequence
    #
    # This is similar to the variant above, but it will work on the
    # aminoacid sequence. This explains the leading "aa", which
    # is short for "aminoacid".
    #
    # Usage example:
    #
    #   setdna 99; aa22..44
    #
    # ===================================================================== #
    when /^aa\[?([0-9,.]{0,9}\d{1,9})\s*[-.,]{1,4}\s*([0-9,.]{1,9})\]?$/
      show_this_subsequence($1, $2, aminoacid_sequence?)
    # ===================================================================== #
    # === gui_restriction_enzymes
    # ===================================================================== #
    when 'gui_restriction_enzymes','guirestrictionenzymes'
      enable_gtk
      ::Bioroebe::RestrictionEnzymes.start_gui_application
    # ===================================================================== #
    # === 2
    # ===================================================================== #
    when '2','restriction_enzymes','2_restriction_enzymes_run'
      load_gtk
      thread = Thread.new { restriction_enzymes_run }
      thread.join
    # ===================================================================== #
    # === bioroebe --hamming-gui
    # ===================================================================== #
    when /^-?-?hamming(_|-| )?gui$/i
      require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
      Thread.new {
        Bioroebe::GUI::Gtk::HammingDistance.run
      }
    # ===================================================================== #
    # === bioroebe --gtk-sizeseq
    # ===================================================================== #
    when /^-?-?gtk(_|-| )?sizeseq$/i
      require 'bioroebe/gui/gtk3/sizeseq/sizeseq.rb'
      Bioroebe::GUI::Gtk::Sizeseq.run
    # ===================================================================== #
    # === bioroebe --gtk-hamming
    # ===================================================================== #
    when /^-?-?gtk(_|-| )?hamming$/i
      require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
      Bioroebe::GUI::Gtk::HammingDistance.run
    # ===================================================================== #
    # === pwd
    # ===================================================================== #
    when 'pwd',
         'pdw',
         /^report(_|-)?current(_|-)?working(_|-)?directory$/i
      report_current_working_directory
    # ===================================================================== #
    # === restriction_table?
    # ===================================================================== #
    when /^restriction(_|-)?table\??/,
         /^show(_|-)?restriction(_|-)?table$/
      show_restriction_table
    # ===================================================================== #
    # === dna_weight?
    # ===================================================================== #
    when /dna_?weight\??/,'weight_of_dna_string',
         'weight?',
         'weight',
         'mweight',
         'show_and_calculate_weight_of_dna_string',
         'molwt',
         'show_individual_weight_of_the_four_dna_nucleotides'
      show_and_calculate_weight_of_dna_string_or_aminoacid_sequence(f)
    # ===================================================================== #
    # === dna_analyze?
    #
    # This entry-point can be used to analyze the given DNA strand at hand.
    # ===================================================================== #
    when 'dna_analyze?',
         'analyse',
         'ana',
         /^stats\??$/i,
         'display',
         'stat?',
         'stat',
         'dnaanalyze?',
         'frequencies',
         'frequencies?',
         'statistics?',
         'analyze_dna_string',
         'frequency',
         'superanalyze',
         /^dna(-|_| )?analyse$/i
      analyze_dna_string(a?)
    # ===================================================================== #
    # === tologdir
    # ===================================================================== #
    when /^to(_|-)?log(_|-)?dir$/,
         /^to(_|-)?log$/
      cd log_dir?
    # ===================================================================== #
    # === create_file
    #
    # This entry point allows the user to create a new file.
    # ===================================================================== #
    when /^create(_|-)?file$/,
         'touch'
      create_file(a?)
    # ===================================================================== #
    # === assign_aa
    # ===================================================================== #
    when /^assign(_|-)?aa$/,
         'aaa'
      assign_aminoacid_sequence(a?)
    # ===================================================================== #
    # === --create-jar
    # ===================================================================== #
    when /^-?-?create(_|-)?jar$/i,
         /^-?-?jar$/i
      ::Bioroebe.create_jar_archive
    # ===================================================================== #
    # === help
    # ===================================================================== #
    when 'hel',
         'he','showhelp',
         /^-?-?help$/i,
         'hep',
         'hepl','elp',
         'show_help',
         '?',
         'hlep' # 'h' is reserved already.
      show_help(f)
    # ===================================================================== #
    # === bioroebe --gtk21
    #
    # This is for show_codon_usage.
    # ===================================================================== #
    when /^-?-?gtk21$/i
      require 'bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb'
      Bioroebe::GUI::Gtk::ShowCodonUsage.run
    # ===================================================================== #
    # === bioroebe --gtk22
    #
    # This is for sizeseq.
    # ===================================================================== #
    when /^-?-?gtk22$/i
      require 'bioroebe/gui/gtk3/sizeseq/sizeseq.rb'
      Bioroebe::GUI::Gtk::Sizeseq.run
    # ===================================================================== #
    # === bioroebe --gtk23
    #
    # This is for three_to_one.
    # ===================================================================== #
    when /^-?-?gtk23$/i
      require 'bioroebe/gui/gtk3/three_to_one/three_to_one.rb'
      Bioroebe::GUI::Gtk::ThreeToOne.run
    # ===================================================================== #
    # === bioroebe --gtk24
    #
    # This is for www_finder.
    # ===================================================================== #
    when /^-?-?gtk24$/i
      require 'bioroebe/gui/gtk3/www_finder/www_finder.rb'
      Bioroebe::GUI::Gtk::WwwFinder.run
    # ===================================================================== #
    # === gtk3
    # ===================================================================== #
    when 'gtk3',
         'load_gtk_subsection'
      load_gtk
      enable_gtk_section_antisensestrand
    # ===================================================================== #
    # === enable_gtk_section_antisensestrand
    # ===================================================================== #
    when /^enable(_|-)?gtk(_|-)?section(_|-)?antisensestrand$/
      enable_gtk_section_antisensestrand
    # ===================================================================== #
    # === enable_gtk
    # ===================================================================== #
    when /^-?-?enable(_|-)?gtk$/,
         'gtk'
      enable_gtk
    # ===================================================================== #
    # === codon_to_aminoacid
    # ===================================================================== #
    when /^codon(_|-)?to(_|-)?aminoacid$/
      e codon_to_aminoacid(a?)
    # ===================================================================== #
    # === toggle2
    # ===================================================================== #
    when 'toggle2'
      toggle_mode
    # ===================================================================== #
    # === name?
    # ===================================================================== #
    when 'name?',
         /^-?-?show(_|-| )?name(_|-| )?of(_|-| )?the(_|-| )?gene$/i
      show_name_of_the_gene
    # ===================================================================== #
    # === show_memo
    # ===================================================================== #
    when /show_?mnemo/,'mnemo','memo',
         'show_memo',
         'memo?'
      show_mnemo
    # ===================================================================== #
    # === bioroebe --gtk-nucleotide-analyser
    # ===================================================================== #
    when /^-?-?gtk(_|-| )?nucleotide(_|-| )?analyser$/i,
         /^-?-?nucleotide(_|-| )?analyser(_|-| )?gtk$/i
      require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
      Bioroebe::GUI::Gtk::NucleotideAnalyser.run
    # ===================================================================== #
    # === download_fasta
    # ===================================================================== #
    when /^download(_|-| )?fasta$/i,
         'dfasta',
         'dfa',
         'wget'
      download_fasta(a?)
    # ===================================================================== #
    # === Handle 33..55 and 33-55 and [33..55] and [33-55]
    #
    # This entry point can be used to obtain a subsequence of our target
    # sequence - it can "handle ranges".
    #
    # See the following link for an explanation of this regex:
    #
    #   https://rubular.com/r/zP7khUUIyC3zA0
    #
    # ===================================================================== #
    when /^\[?([0-9,.]{0,9}\d{1,9})\s*[-.,]{1,4}\s*([0-9,.]{1,9})\]?$/
      show_this_subsequence($1, $2)
    # ===================================================================== #
    # === blosum90
    # ===================================================================== #
    when /^-?-?blosum90/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === calculate_levensthein
    # ===================================================================== #
    when /calculate(_|-| )?levensthein(_|-| )?distance/i,
         'calculate_levensthein' # lst computation complication
      ::Bioroebe.calculate_levensthein_distance(a?) # This will output the result by default.
    # ===================================================================== #
    # === longest_substring
    # ===================================================================== #
    when /longest(_|-)?substring/,
         'find_substring',
         'substring',
         'sub'
      find_longest_substring(a?) # sub AAAAGATAAACAAAAGGGG ATATCCTAAACAAAAGGGG
    # ===================================================================== #
    # === set_xclip
    # ===================================================================== #
    when /^set(_|-)?xclip$/i,
         'set_buffer',
         'xclip',
         'buffer',
         /^to(_|-)?buffer/i,
         'xorgbuffer',
         'setxorg'
      erev 'Next assigning the main DNA sequence to the Xorg Buffer.'
      set_xclip
    # ===================================================================== #
    # === to_base
    # ===================================================================== #
    when /to(_|-)?base$/,
         'base',
         /enter_?base_?dir/
      enter_base_directory
    # ===================================================================== #
    # === three_to_one
    #
    # This entry point will convert the three-letter code to the
    # one-letter code (in regards to aminoacids).
    #
    # Invocation example:
    #
    #   3to1 ARG-ALA-SER-LEU-PHE-TRP-LYS-HIS-ASN-SER-VAL-LEU-ILE-VAL-PRO
    #
    # ===================================================================== #
    when /^three(_|-)?to(_|-)?one$/,
         '3-1',
         '3letters',
         /^3(_|-| )?to(_|-| )?1$/ # === 3to1
      three_to_one(a?)
    # ===================================================================== #
    # === oligo_three
    # ===================================================================== #
    when /^oligo(_|-)?three$/,
         'oligo_length_three',
         'oligolengththree',
         'three',
         /^show(_|-)?oligo(_|-)?length(_|-)?three$/,
         'oligo_3',
         'oligo3'
      show_oligo_length_three
    # ===================================================================== #
    # === random_insert
    # ===================================================================== #
    when /^random(_|-)?insert$/i,
         'rinsert'
      random_insert(a?)
    # ===================================================================== #
    # === 9cut
    # ===================================================================== #
    when /^\d+cut$/,
         /^cut\d+$/, # Example: "9cut" or "cut9".
         /^cut(_|-)?sequence(_|-)?in(_|-)?slices(_|-)?of$/i
      _ = f.to_s.gsub(/cut/,'')
      cut_sequence_in_slices_of(_)
    # ===================================================================== #
    # === runmode?
    # ===================================================================== #
    when /runmode?/
      e runmode?
    # ===================================================================== #
    # === subseq2
    #
    # Usage example:
    #
    #   set_raw_sequence ATGCATGCAAA; subseq2
    #
    # ===================================================================== #
    when /^-?-?subseq2$/i
      show_this_subsequence(2, 4, raw_sequence?)
      # ===================================================================== #
      # === set_raw_sequence
      #
      # Usage example:
      #
      #   set_raw_sequence ATGCATGCAAA; raw_sequence?
      #   setrawsequence ATGCATGCAAA; raw_sequence?
      #
      # ===================================================================== #
    when /^-?-?set(_|-| )?raw(_|-| )?sequence$/i,
         /^-?-?assign(_|-| )?raw$/i
      erev 'Now assigning to the new sequence '+sfancy(f)
      set_raw_sequence(f)
    # ===================================================================== #
    # === annotate
    # ===================================================================== #
    when 'annotate'
      annotate_this_file(f)
    # ===================================================================== #
    # === hydropathy_table?
    # ===================================================================== #
    when 'hydropathy_table?',
         'hydropathytable?',
         'show_hydropathy_table',
         'showhydropathytable',
         'hydropathy?',
         /hpathy\??/,
         'spathy',
         'hydropathy_table',
         'hytable'
      show_hydropathy_table
    # ===================================================================== #
    # === restriction_sizes
    # ===================================================================== #
    when /^restriction(_|-)?sites$/i,
         'rest',
         'restriction',
         'sites',
         'res',
         'show_restriction_enzymes',
         'enzymes',
         'enz',
         'enzymes?',
         'rest2',
         'r',
         '4',
         'srest',
         'allrest',
         'show_rests'
      show_restriction_enzymes(:show_all) unless f
      find_restriction_sites(f) if f # Only do this if an argument was passed.
      @internal_hash[:bioroebe] << a.upcase if a
      @internal_hash[:bioroebe].restriction_sites?(dna_sequence?)
    # ===================================================================== #
    # === do_not_show_the_leader
    # ===================================================================== #
    when /^-?-?do_?not_?show_?the_?leader$/i,
         /^-?-?no_?leader$/i
      do_not_show_the_leader
    # ===================================================================== #
    # === readline?
    # ===================================================================== #
    when 'readline?'
      report_whether_readline_is_available
    # ===================================================================== #
    # === iaminoacid?
    # ===================================================================== #
    when 'iaminoacid?',
         /^identify(_|-)?aminoacid$/i,
         'iaminoacid',
         'aminoacid'
      identify_aminoacid(a?)
    # ===================================================================== #
    # === kozak?
    # ===================================================================== #
    when /^kozak\??$/i
      e
      erev '  GCCACCAUGG'
      e
    # ===================================================================== #
    # === first_atg?
    #
    # This entry point will show where the first ATG can be found in a
    # given sequence.
    # ===================================================================== #
    when /^first(_|-)?atg\??/i,
         /^report(_|-)?the(_|-)?first(_|-)?atg$/i
      report_the_first_atg
    # ===================================================================== #
    # === insulin
    #
    # This quick-link is used mostly just to quickly jump to the
    # insulin sequence.
    # ===================================================================== #
    when 'insulin'
      _ = NCBI_NUCCORE+'NC_000011.10?report=fasta&from=2159779&to=2161209&strand=true'
      e _
      open_in_browser _
    # ===================================================================== #
    # === Handle numbers given as input
    #
    # This entry point can be used to match numbers, such as 33 or
    # 66.
    # ===================================================================== #
    when /^[0-9]+$/
      assign(i)
    # ===================================================================== #
    # === assign_protein
    # ===================================================================== #
    when /^assign(_|-)?protein$/,
         /^assign(_|-)?aminoacids$/,
         'aprotein'
      assign_protein_sequence(a?)
    # ===================================================================== #
    # === show_complement
    # ===================================================================== #
    when 'show_complement',
         'complement',
         'complement?',
         'complementary',
         'cment',
         'c?',
         'co',
         'clent',
         'compl',
         'partner'
      show_complement(all_arguments?, :show_leading_primes)
    # ===================================================================== #
    # === ensure_that_the_base_directories_exist
    # ===================================================================== #
    when /^ensure(_|-)?that(_|-)?the(_|-)?base(_|-)?directories(_|-)?exist$/i
      erev 'Now creating some '+steelblue('base directories')+rev+
           ' for the bioroebe project.'
      Bioroebe.ensure_that_the_base_directories_exist
    # ===================================================================== #
    # === sizeseq
    # ===================================================================== #
    when /sizeseq/
      run_sizeseq
    # ===================================================================== #
    # === frame123
    # ===================================================================== #
    when 'frame123'
      showorf(dna_sequence?, :frame1_frame2_frame3)
    # ===================================================================== #
    # === find_restriction_sites
    # ===================================================================== #
    when 'find_restriction_sites',
         'rest?',
         'findrestrictionsites'
      find_restriction_sites(string?)
    # ===================================================================== #
    # === 1mbo
    # ===================================================================== #
    when /^1mbo$/
      download_this_pdb_file('1mbo')
    # ===================================================================== #
    # === no_truncate
    # ===================================================================== #
    when /^dont(_|-)?truncate$/,
         'do_not_truncate',
         'donottruncate',
         'no_truncate',
         'notruncate',
         'truncate-',
         '-truncate',
         '-trunc'
      do_not_truncate
    # ===================================================================== #
    # === pstop
    # ===================================================================== #
    when 'pstop',
         'astop'
      append_stop_codon
    # ===================================================================== #
    # === create_fasta
    # ===================================================================== #
    when /^create(_|-)?fasta$/i,
         /^make(_|-)?fasta$/i,
         /^save(_|-)?fasta$/i,
         /^create_?fasta_?file/
      create_fasta_file
    # ===================================================================== #
    # === K12
    # ===================================================================== #
    when 'K12'
      show_Ecoli_K12_information
    # ===================================================================== #
    # === test10
    # ===================================================================== #
    when 'test10'
      # =================================================================== #
      # Just some testing here.
      # =================================================================== #
      dna = ::Bioroebe::DNA.new(string?)
      find_this_subsequence = 'ATG'
      e 'Looking for '+royalblue(find_this_subsequence)
      array = dna.find_this_subsequence find_this_subsequence
      pp array
    # ===================================================================== #
    # === atgccontent
    # ===================================================================== #
    when 'atgccontent',
         'atcgcontent',
         'ncontent',
         'tacgcontent'
      calculcate_at_content(a?)
      calculcate_gc_content(a?)
    # ===================================================================== #
    # === use_fasta
    # ===================================================================== #
    when /^use_?fasta$/i,
         'use_this_fasta',
         'ufasta',
         'usethisfasta',
         'use_this_fasta_file',
         'useasta'
      use_this_fasta_file(f) # Use a fasta file based on its position.
    # ===================================================================== #
    # === The ViennaRNA package
    # ===================================================================== #
    when 'b2ct',
         'ct2db',
         'Kinfold',
         'popt',
         'RNA2Dfold',
         'RNAaliduplex',
         'RNAalifold',
         'RNAcofold',
         'RNAdistance',
         'RNAduplex',
         'RNAeval',
         'RNAfold',
         'RNAforester',
         'RNAheat',
         'RNAinverse',
         'RNALalifold',
         'RNALfold',
         'RNAlocmin',
         'RNApaln',
         'RNAparconv',
         'RNApdist',
         'RNAPKplex',
         'RNAplex',
         'RNAplfold',
         'RNAplot',
         'RNApvmin',
         'RNAsnoop',
         'RNAsubopt',
         'RNAup'
      this_command = i.dup+' '
      if a
        this_command << a.join(' ').chomp
      end
      e
      esystem(this_command)
      e
    # ===================================================================== #
    # === restore
    #
    # This will restore the last chop-operation.
    # ===================================================================== #
    when 'restore'
      restore_the_last_chop_operation
    # ===================================================================== #
    # === mirror_repeat
    # ===================================================================== #
    when /^mirror(_|-)?repeat$/i,
         /^mirror$/i
      mirror_repeat(a?)
    # ===================================================================== #
    # === TTAA
    # ===================================================================== #
    when 'TTAA?',
         'TTAA',
         'TTA_transposon'
      show_colourized_sequence('TTAA')
    # ===================================================================== #
    # === count_nucleotides
    # ===================================================================== #
    when 'cnucleotides',
         /count_?nucleotides/
      ::Bioroebe::CountAmountOfNucleotides.new(f) # cnucleotides ATTGGCTTGCCGGCAGACGA
    # ===================================================================== #
    # === all_sequences?
    # ===================================================================== #
    when 'all_sequences?',
         'allsequences?'
      show_main_dna_sequence # We show them only when they are NOT empty.
      show_seq_2 unless seq2?.empty?
      show_seq_3 unless seq3?.empty?
      show_seq_4 unless seq4?.empty?
      show_seq_5 unless seq5?.empty?
      show_seq_6 unless seq6?.empty?
    # ===================================================================== #
    # === CAP?
    # ===================================================================== #
    when 'CAP?',
         'CAP',
         'cap',
         'cap?'
      try_to_find_restriction_enzymes_for('TGTGA') # See: http://www.jbc.org/content/261/23/10885.full.pdf
    # ===================================================================== #
    # === unfreeze
    # ===================================================================== #
    when /^unfreeze$/,
         /^unfrozen$/,
         /^unfreeze(-|_| )?the(-|_| )?main(-|_| )?sequence$/
      erev 'Unfreezing the main sequence next.'
      unfreeze_the_main_sequence
    # ===================================================================== #
    # === show_editor_in_use
    # ===================================================================== #
    when /^show(_|-)?editor(_|-)?in(_|-)?use$/,
         'editor?',
         'ed?'
      show_editor_in_use
    # ===================================================================== #
    # === Mus_musculus.GRCm38.75.gtf.gz
    # ===================================================================== #
    when 'Mus_musculus.GRCm38.75.gtf.gz'
      download(
        'ftp://ftp.ensembl.org/pub/release-75/gtf/mus_musculus/Mus_musculus.GRCm38.75.gtf.gz'
      )
    # ===================================================================== #
    # === dump
    # ===================================================================== #
    when /^dump$/i
      dump(a?)
    # ===================================================================== #
    # === seq2?
    # ===================================================================== #
    when 'seq2?',
         's2?',
         /^show_?seq_?2/
      show_seq_2
    # ===================================================================== #
    # === seq2
    # ===================================================================== #
    when 'seq2'
      assign_sequence2(a?)
    # ===================================================================== #
    # === index_this_fasta_file
    #
    # This entry point will use samtools to index .fasta file(s).
    #
    # If no argument is given then this method will, by default, try
    # to use all .fasta and .fa files from the current working
    # directory. This feature exists primarily for convenience.
    # ===================================================================== #
    when /^-?-?index(_|-)?this(_|-)?fasta(_|-)?file$/i,
         /^-?-?index$/i
      index_this_fasta_file(a?) { :use_all_fasta_files_if_no_argument_was_given }
    # ===================================================================== #
    # === sanitize_nucleotide_sequence
    # ===================================================================== #
    when /^sanitize(_|-)?nucleotide(_|-)?sequence$/
      sanitize_nucleotide_sequence(a?)
    # ===================================================================== #
    # === align_ORFS
    # ===================================================================== #
    when /^align_?ORFS/i,'alignmorfs',
          'pretty_orf',
         /^align_?open_?reading_?frames/
      align_ORFS # Show all ORFs properly aligned.
    # ===================================================================== #
    # === pcr?
    # ===================================================================== #
    when 'pcr?'
      calculate_melting_temperature :show_formulas
    # ===================================================================== #
    # === completions?
    # ===================================================================== #
    when 'completions?','complet?'
      if use_readline?
        show_readline_completions
      else
        erev 'No completions are known, as the readline '\
             'module is not in use.'
      end
    # ===================================================================== #
    # === phred_quality_score_table
    # ===================================================================== #
    when /phred(_|-)?quality(_|-)?score(_|-)?table/
      require 'bioroebe/ngs/phred_quality_score_table.rb'
      ::Bioroebe::PhredQualityScoreTable.new
    # ===================================================================== #
    # === cuts_at?
    #
    # Where restriction enzymes cut.
    # ===================================================================== #
    when 'cuts_at?',
         'cuts_at',
         'cut?',
         'r?',
         'find_restriction_enzymes_that_cut_at',
         'findcutat?',
         'cutsat?'
      find_restriction_enzymes_that_cut_at(a?)
    # ===================================================================== #
    # === delimiter
    # ===================================================================== #
    when /delimiter/
      show_sequence_in_splitted_form(f) {{ use_this_token: '|' }}
    # ===================================================================== #
    # === aaruler
    #
    # Usage example:
    #
    #   aaruler KLKLKLKLAALKLAKLA
    #
    # ===================================================================== #
    when /^aaruler$/
      _ = aminoacid_sequence? # Default value.
      if f and !f.nil? and !f.empty?
        _ = f
      end
      show_sequence_with_a_ruler(:default, _, :aminoacids)
    # ===================================================================== #
    # === ruler
    #
    # This entry point will display a useful number on each nucleotide
    # position.
    # ===================================================================== #
    when /^ruler$/,
         /^-?-?show(_|-| )?sequence(_|-| )?with(_|-| )?a(_|-| )?ruler$/
      show_sequence_with_a_ruler(a?, :default, :dna)
    # ===================================================================== #
    # === e
    #
    # This entry point can be used to quickly feedback which arguments
    # have been passed.
    #
    # Specific usage example:
    #
    #   e one two three
    #
    # ===================================================================== #
    when 'e'
      e all_arguments?
    # ===================================================================== #
    # === check_for_mismatches
    # ===================================================================== #
    when /^check(_|-)?for(_|-)?mismatches$/i,
         'mismatch',
         'mismatches'
      check_for_mismatches
    # ===================================================================== #
    # === bedtoolsv
    # ===================================================================== #
    when 'bedtoolsv',
         'bedtools?',
         /^try(_|-)?to(_|-)?report(_|-)?the(_|-)?version(_|-)?of(_|-)?bedtools$/
      try_to_report_the_version_of_bedtools
    # ===================================================================== #
    # === return_random_nucleotide
    # ===================================================================== #
    when /^return(_|-)?random(_|-)?nucleotide$/i
      e return_random_nucleotide
    # ===================================================================== #
    # === return_random_aminoacid
    # ===================================================================== #
    when /^return(_|-)?random(_|-)?aminoacid$/i
      e return_random_aminoacid
    # ===================================================================== #
    # === cut_with_enzyme
    #
    # This entry point can be used to cut a DNA sequence with a
    # restriction enzyme.
    #
    # Invocation example:
    #
    #   cut_with_enzyme EcoRI
    #
    # ===================================================================== #
    when /^cut(_|-)?with(_|-)?enzyme$/i
      cut_with_enzyme(a?)
    # ===================================================================== #
    # === show_history
    #
    # This entry point can be used to show the input-history that was
    # used so far. The "input-history" is what the user typed.
    # ===================================================================== #
    when /^show(_|-)?history$/i,
         'h',
         'h?',
         'history',
         'history?',
         'hist',
         'hist?'
      show_history
    # ===================================================================== #
    # === try_to_find_this_restriction_enzyme
    # ===================================================================== #
    when /^try(_|-)?to(_|-)?find(_|-)?this(_|-)?restriction(_|-)?enzyme$/
      try_to_find_this_restriction_enzyme(f)
    # ===================================================================== #
    # === dalton
    # ===================================================================== #
    when /^dalton$/i
      dalton(f?)
    # ===================================================================== #
    # === search_for
    # ===================================================================== #
    when /^search(_|-)?for$/ 
      search_for(a?)
    # ===================================================================== #
    # === colour_test
    # ===================================================================== #
    when /^colour(_|-)?test$/i
      set_highlight_colour(:violet)
    # ===================================================================== #
    # === to_dna
    # ===================================================================== #
    when /^to(_|-| )?DNA$/i,
         'dna',
         'rna2dna'
      to_dna(f)
    # ===================================================================== #
    # === backtranseq
    #
    # This entry point allows us to translate an Aminoacid Sequence back
    # into the most likely DNA sequence.
    #
    # Usage example:
    #
    #   backtranseq ARGARG
    #
    # ===================================================================== #
    when 'backtranseq',
         'backseq',
         'backtrack',
         /^aminoacid(_|-| )?to(_|-| )?dna$/i,
         'runcodons',
         'btrack',
         /^protein(_|-| )?to(_|-| )?dna$/i,
         'proteintodna',
         'p_to_d','ptod',
         /^reverse(_|-| )?dna$/i,
         /^reverse(_|-| )?seq$/i,
         /^reverse(_|-| )?aa$/i, # === reverse_aa
         'bseq',
         'backtraq',
         'backtrach'
      backtranseq(a?)
    # ===================================================================== #
    # === colour_test
    # ===================================================================== #
    when /^colour(_|-)?test/
      e
      erev 'This is a test.'
      e
      erev 'This is another test.'
      erev 'Now for '+slateblue('slateblue')+rev+'.'
      erev 'Now for '+lightgreen('lightgreen')+rev+'.'
      e
    # ===================================================================== #
    # === show_aminoacids_mass_table
    # ===================================================================== #
    when /^show(_|-)?aminoacids(_|-)?mass(_|-)?table$/i,
         /^show(_|-)?aminoacid(_|-)?mass$/i,
         'showmass',
         'aminoacid_table_overview',
         'aminomass',
         'aminomasses'
      show_aminoacids_mass_table
    # ===================================================================== #
    # === stride
    # ===================================================================== #
    when 'stride' # The C-program called stride.
      _ = 'stride '+f?.to_s+' > '+f?.to_s+'_stride_output'
      esystem(_)
    # ===================================================================== #
    # === multliline_assignment
    # ===================================================================== #
    when /^multiline_?assignment$/,
         'mass',
         'multiline2',
         'mline',
         'mmm',
         '___',
         '__',
         '--',
         'assignmultiline',
         'assign_multiline',
         'multiline_input',
         'multilineinput',
         'multi_line',
         'multiline',
         'multi-line',
         'multi_input',
         'multline'
      assign_sequence(:multiline)
    # ===================================================================== #
    # === download_dir?
    # ===================================================================== #
    when /^download(_|-)?dir\??$/,
         'ddir?','base?',
         'depotdir?','depot?',
         /^temp\??$/i,
         /^show(_|-)?download(_|-)?dir$/ # === show_download_dir
      show_download_dir
    # ===================================================================== #
    # === @parse_fasta
    # ===================================================================== #
    when '@parse_fasta'
      last_fasta_entry?.display
    # ===================================================================== #
    # === show_aa
    # ===================================================================== #
    when /^show(_|-)?aa$/i,
         'aminoacids?','aaseq?','aasq?','aminacids?',
         'aminocids?',
         'aasequence?',
         /^show(_|-)?aminoacid(_|-)?sequence$/i
      show_aminoacid_sequence
    # ===================================================================== #
    # === pyrrolysine
    # ===================================================================== #
    when /pyrrolysine?\??/
      erev 'UAG codes for pyrrolysine'
    # ===================================================================== #
    # === to_T
    #
    # Convert all 'U' into 'T', if there are any U at all.
    # ===================================================================== #
    when /^to(_|-)?T$/i
      dna_sequence_object?.extend(Bioroebe::NucleotideModule)
      assign_this_dna_sequence(
        dna_sequence_object?.to_T
      )
    # ===================================================================== #
    # === theory?
    # ===================================================================== #
    when 'theory','theory?'
      e '  T = h ** 2 + h*k + k ** 2'
    # ===================================================================== #
    # === ..
    # ===================================================================== #
    when '..'
      cd '..'
    # ===================================================================== #
    # === last_inputted_command?
    # ===================================================================== #
    when /^last(_|-)?inputted(_|-)?command\??$/i
      e last_inputted_command?
    # ===================================================================== #
    # === flybase?
    # ===================================================================== #
    when /^flybase\??$/i
      open_in_browser(i.delete('?'))
    # ===================================================================== #
    # === fasta_file?
    # ===================================================================== #
    when /^fasta(_|-)?file\??$/i
      e fasta_file?
    # ===================================================================== #
    # === dna?
    # ===================================================================== #
    when 'dnaa?',
         'dnaA',
         'dnaA?'
      attempt_to_discover_dna_A_boxes
    # ===================================================================== #
    # === useful_packages?
    # ===================================================================== #
    when /^useful(_|-)?packages\??$/,
         /^science(_|-)?addons\??$/,
         /^addons\??$/,
         /^external\??$/,
         /^status\??$/,
         /^report$/
      report_useful_packages_installed
    # ===================================================================== #
    # === f23
    # ===================================================================== #
    when 'f2,f3','f23'
      showorf(dna_sequence?, :frame2_frame3)
    # ===================================================================== #
    # === f1,f2
    # ===================================================================== #
    when 'f1,f2','f12'
      showorf(dna_sequence?, :frame1_frame2)
    # ===================================================================== #
    # === f1,f2,f3
    # ===================================================================== #
    when 'f1,f2,f3'
      showorf(dna_sequence?, :frame1_frame2_frame3)
    # ===================================================================== #
    # === genbank?
    # ===================================================================== #
    when 'genbank?'
      open_in_browser :genbank
    # ===================================================================== #
    # === gold?
    # ===================================================================== #
    when 'gold?'
      _ = 'https://gold.jgi.doe.gov/'
      e _
      open_in_browser(_)
    # ===================================================================== #
    # === purge
    # ===================================================================== #
    when 'purge'
      purge(a?)
    # ===================================================================== #
    # === restrictionenzymes?
    # ===================================================================== #
    when 'restrictionenzymes?','restrictionenzymes','restriction?'
      show_restriction_enzymes(:show_all)
    # ===================================================================== #
    # === longest_ORF
    # ===================================================================== #
    when /^longest(_|-| )?ORF$/i
      _ = Bioroebe.longest_ORF?(sequence_as_string?)
      erev 'The longest ORF has a size of '+steelblue(_.size.to_s)+
           rev+' nucleotides.'
      erev 'This sequence is shown next:'
      e
      show_this_sequence(_)
      e
    # ===================================================================== #
    # === codon_usage_database?
    # ===================================================================== #
    when /^codon(_|-)?usage(_|-)?database\??$/i
      erev 'On 20.05.2016 this database has had:'
      e
      erev '  35,799 organisms'
      erev "  3,027,973 complete protein coding genes (CDS's)"
      e
    # ===================================================================== #
    # === 1IGT
    #
    # This .pdb file is related to antibodies.
    # ===================================================================== #
    when '1IGT'
      open_1igt_in_the_browser
    # ===================================================================== #
    # === enable_xsel
    # ===================================================================== #
    when /^enable(_|-)?xsel$/i
      enable_xsel
    # ===================================================================== #
    # === show_xorg_buffer
    # ===================================================================== #
    when /^show(_|-)?xorg(_|-)?buffer$/i,
         /^show(_|-)?xbuffer$/i,
         'sxorgbuffer'
      show_xorg_buffer
    # ===================================================================== #
    # === weight_of_nucleotides
    #
    # This entry point simply shows the weight of the four different
    # nucleotides.
    # ===================================================================== #
    when /^weight(_|-)?of(_|-)?nucleotides$/i,
         /^wnuc$/i
      show_the_weight_of_the_four_individual_nucleotides
    # ===================================================================== #
    # === viennarnav
    # ===================================================================== #
    when /^viennarna(v|\?)?$/i # Allows both "viennarna" and "viennarna?"
      try_to_report_the_version_of_viennarna
    # ===================================================================== #
    # === yaml?
    # ===================================================================== #
    when 'yaml','yaml?',
         /^show(_|-)?all(_|-)?yaml(_|-)?files/i
      show_all_yaml_files
    # ===================================================================== #
    # === match_pattern
    #
    # Usage example:
    #
    #   match_pattern ACGTACGTAACG GTA
    #   match_pattern ATGTGACTACGACGCATATGACGTACGTAACG ATG
    # 
    # ===================================================================== #
    when /^match(_|-)?pattern$/i
      results = Bioroebe.return_array_of_sequence_matches(
        first_argument?, second_argument?
      )
      results.reverse.each {|position|
        show_this_sequence(
          first_argument?[(position-1) .. -1]
        )
      }
    # ===================================================================== #
    # === to_genbank
    #
    # This entry point can be used to convert the main DNA sequence to
    # the genbank format.
    # ===================================================================== #
    when /^to(_|-)?genbank$/,
         'togen',
         'filemaker',
         'format?',
         'genbeauty',
         'beauty2',
         'togenb',
         'genbank',
         'togenban',
         'genbankflatfilegen',
         'formatter',
         'pretty',
         'prettify',
         'beautify',
         'sanitize',
         /table_?formatter/
      to_genbank
    # ===================================================================== #
    # === last_update?
    #
    # This entry point notifies the user as to when the bioroebe project
    # was last updated.
    # ===================================================================== #
    when /^last(_|-)?update\??$/i
      report_when_the_bioroebe_project_was_last_updated
    # ===================================================================== #
    # === colour_scheme
    #
    # Usage example:
    #
    #   colour_scheme ATGACTCAGACACTAGCTAGCTAGCTAGACTACA
    #
    # ===================================================================== #
    when /^colour(_|-)?scheme$/i,
         /^colour(_|-)?scheme(_|-)?for(_|-)?nucleotides$/i,
         'cscheme'
      colour_scheme_for_nucleotides(a?)
    # ===================================================================== #
    # === constants?
    # ===================================================================== #
    when 'constants?'
      pp ::Bioroebe.constants.sort
    # ===================================================================== #
    # === config?
    # ===================================================================== #
    when 'config?',
         'configuration?',
         'con?',
         'show_config',
         'showconfig'
      try_to_show_the_configuration
    # ===================================================================== #
    # === swisss-prot?
    # ===================================================================== #
    when /swiss-?prot\??/,
         /report_?n_?proteins_?registered_?in_?swiss_?prot$/
      report_n_proteins_registered_in_swiss_prot
    # ===================================================================== #
    # === rubyversion
    #
    # The second line is for jruby specifically.
    # ===================================================================== #
    when /^ruby(_|-)?version/i
      e steelblue(RUBY_VERSION)
      if Object.const_defined?(:ENV_JAVA)
        erev 'Java version: '+
             steelblue(ENV_JAVA['java.version'].to_s)
      end
    # ===================================================================== #
    # === disable
    #
    # This entry point allows us to disable specific features, as far
    # as the BioRoebe shell is concerned.
    # ===================================================================== #
    when /^disable/,
         'no'
      disable(a?)
    # ===================================================================== #
    # === shine_dalgarno?
    # ===================================================================== #
    when 'shine_dalgarno?','shine?',
         'shine',
         'shine_dalgarno',
         'sd',
         'sd?',
         'find_shine_dalgarno_sequence',
         'sine'
      find_shine_dalgarno_sequence
    # ===================================================================== #
    # === random_dna_sequence
    #
    # This entry point will simply display the random DNA sequence,
    # the default length. Currently this is 250.
    # ===================================================================== #
    when /^random(_|-)?dna(_|-)?sequence$/i
      display_this_nucleotide_sequence(
        random_dna_sequence
      )
    # ===================================================================== #
    # === raw?
    # ===================================================================== #
    when 'raw?','raw'
      show_dna_string(
        dna_string?, :do_not_truncate_and_do_not_show_leader_and_trailer
      )
    # ===================================================================== #
    # === salt_adjusted_tm
    #
    # Entry point for calculating the salt-adjust Tm (melting temperature).
    #
    # Most useful for primers in the range of 18-25, give or take.
    # ===================================================================== #
    when /^salt(_|-)?adjusted(_|-)?tm$/,
         /^melting(_|-)?temperature2$/
      erev salt_adjusted_tm(a?)
    # ===================================================================== #
    # === melting_temperature?
    # ===================================================================== #
    when 'calculate_melting_temperature','calculatemeltingtemperature',
         'mt','melting_temperature','ctemp','tm','melting?',
         'melting_temperature?','melt',
         'cmelt','calmelt'
      calculate_melting_temperature(a?) # melting? GCCGCGGTTTCGGGA
    # ===================================================================== #
    # === translate3
    # ===================================================================== #
    when 'translate3','t','aminoacid?','trans1'
      translate(a?)
    # ===================================================================== #
    # === bioroebe --libui1
    #
    # All --libui entries should be sorted alphabetically in this
    # menu as well.
    # ===================================================================== #
    when /^-?-?libui1?$/i
      require 'bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
      Bioroebe::GUI::LibUI::DnaToAminoacidWidget.run
    # ===================================================================== #
    # === bioroebe --libui2
    # ===================================================================== #
    when /^-?-?libui2$/i
      require 'bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
      Bioroebe::GUI::LibUI::DnaToAminoacidWidget.run
    # ===================================================================== #
    # === bioroebe --libui3
    # ===================================================================== #
    when /^-?-?libui3$/i
      require 'bioroebe/gui/libui/random_sequence/random_sequence.rb'
      Bioroebe::GUI::LibUI::RandomSequence.run
    # ===================================================================== #
    # === show_taxid
    # ===================================================================== #
    when 'show_taxid','showtaxid','taxid?','taxid'
      show_taxid(a?)
    # ===================================================================== #
    # === ten_split
    # ===================================================================== #
    when /^ten(_|-)?split$/i
      show_sequence_in_splitted_form(10)
    # ===================================================================== #
    # === n_downloads?
    # ===================================================================== #
    when 'n_downloads?' # How often Bioroebe was downloaded.
      require 'bestgems'
      n_times = Bestgems.client.total_downloads(:bioroebe).values.first
      erev 'The Bioroebe project has been downloaded '+simp(n_times.to_s)+rev+' times.'
    # ===================================================================== #
    # === genbank_version?
    # ===================================================================== #
    when /genbank_?version\??/,'report_current_genbank_version',
         'top',
         'genebank?',
         'reportcurrentgenbankversion',
         'genbankversion?',
         'genbank_version',
         'current_genbank_version?',
         'current_genbank_version'
      report_current_genbank_version(:also_report_the_URL)
    # ===================================================================== #
    # === phosphorylation_sites?
    # ===================================================================== #
    when 'phosphorylation_sites?','psites?','phosphorylationsites?',
         'phosphorylationsites','psites','phosphorylation_site?',
         'phospho?','show_phosphorylation_sites','showphosphorylationsites',
         'p?','P',
         'phosphorylation',
         'P?'
      show_possible_phosphorylation_sites
    # ===================================================================== #
    # === pitch
    # ===================================================================== #
    when 'pitch','alpha_helix_pitch',
         'alphahelixpitch'
      show_length_of_alpha_helix(a?)
    # ===================================================================== #
    # === handle_pdb_files
    #
    # Invocation example:
    #
    #   handle_pdb_files http://www.rcsb.org/pdb/files/3O30.pdb
    #
    # ===================================================================== #
    when /^handle(_|-)?pdb(_|-)?files$/i,
         'pdb','pdb?',
         'download_pdb',
         'dpdb',
         'downloadpdb',
         /^download(_|-)?this(_|-)?pdb(_|-)?file$/i
      handle_pdb_files(a?)
    # ===================================================================== #
    # === pdburl?
    # ===================================================================== #
    when /pdb(_|-| )?url?/,
         'pdb2?'
      e 'https://www.wwpdb.org/'
    # ===================================================================== #
    # === freeze
    # ===================================================================== #
    when /^freeze$/,
         /^frozen$/,
         /^freeze(-|_| )?the(-|_| )?main(-|_| )?sequence$/
      erev 'Freezing the main sequence next.'
      freeze_the_main_sequence
    # ===================================================================== #
    # === parse
    #
    # This is the general-entry for parse-related activities in regards
    # to the bioshell-interface.
    #
    # Examples for files that are parsed include .pdb files and
    # .fasta files.
    # ===================================================================== #
    when 'parse',
         /^parse(_|-| )?this(_|-| )?pdb(_|-| )?file$/,
         /^parse(_|-| )?pdb(_|-| )?file$/,
         /^parse(_|-| )?pdb$/,
          'parse_fasta_format',
         /^parse(_|-| )?fasta$/,
         'pfasta',
         'pasta',
         'fasta',
         'fast',
         /^assign(_|-| )?fasta$/
      parse(a?)
    # ===================================================================== #
    # === cut_at
    # ===================================================================== #
    when /cut(_|-)?at$/i
      cut_at(f)
    # ===================================================================== #
    # === punnet
    # ===================================================================== #
    when 'punnet',
         'pun'
      punnet(a?) # bl $BIOROEBE/shell/shell.rb
    # ===================================================================== #
    # === stop_frame1?
    # ===================================================================== #
    when /^stop(_|-)?frame1\??$/i
      report_main_sequence(dna_sequence_as_string?, :stop_codon_in_frame1)
    # ===================================================================== #
    # === stop_frame2?
    # ===================================================================== #
    when /^stop(_|-)?frame2\??$/i
      report_main_sequence(dna_sequence_as_string?, :stop_codon_in_frame2)
    # ===================================================================== #
    # === stop_frame3?
    # ===================================================================== #
    when /^stop(_|-)?frame3\??$/i
      report_main_sequence(dna_sequence_as_string?, :stop_codon_in_frame3)
    # ===================================================================== #
    # === orf?
    #
    # This entry point will display to the user where open reading
    # frames can be found in the main sequence.
    # ===================================================================== #
    when /^ORF\??$/i,
         /^ORF1\??$/i,
         /^ORFs\??$/i,
         'open_reading_frames',
         'search?',
         'startcodons?',
         'search_for_orfs',
         'orfs?',
         /^open(_|-)?reading(_|-)?frames$/i,
         'start?',
         'toorf',
         'ORFS?',
         'all_ORFs',
         'allorfs',
         'ATG?',
         /^AUG\??$/i
      result = search_sequence_for_open_reading_frames
      print '  '
      pp result
      e
      # =================================================================== #
      # Colourize all ATG tags next. One day this may have to become
      # more flexible so that we can colourize codons other than ATG,
      # since e. g. in bacteria, a few genes start with another codon.
      # =================================================================== #
      show_nucleotide_sequence?.display(main_sequence?) { :colourize_start_codon }
      e
      if f? # User supplied an argument in this case
        report_n_start_codons { f? }
      else
        report_n_start_codons
      end
    # ===================================================================== #
    # === orf2?
    # ===================================================================== #
    when /^ORF2\??$/i
      result = search_sequence_for_open_reading_frames(
        :default, :frame2, :default
      )
      erev result
    # ===================================================================== #
    # === fastq_quality_scores
    # ===================================================================== #
    when /^fastq(_|-)?quality(_|-)?scores$/i,
         /^fastq(_|-)?quality(_|-)?schemes$/i,
         /^show(_|-)?fastq(_|-)?quality(_|-)?score(_|-)?table$/i,
         /^fastq(_|-)?table?/
      show_fastq_quality_score_table
    # ===================================================================== #
    # === Visit the human GRCh38.p14 assembly
    # ===================================================================== #
    when /^GRCh38.p14$/i
      open_in_browser 'https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.40'
    # ===================================================================== #
    # === Visit the human GRCh38 assembly
    # ===================================================================== #
    when /^GRCh38$/i
      open_in_browser 'https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/'
    # ===================================================================== #
    # === Feedback which browser is in use
    #
    # Usage example:
    #
    #   browser?
    #
    # ===================================================================== #
    when /^browser\??$/i
      e YAML.load_file(project_yaml_directory?+'configuration/browser.yml')
    # ===================================================================== #
    # === one-to-three
    #
    # This will convert from the one-aminoacid letter to the three-aminoacid
    # letter.
    #
    # Usage example:
    #
    #   1to3 KRKAKAGAGAUUGAUGAAGCCACA # => Lys-Arg-Lys-Ala-Lys-Ala-Gly-Ala-Gly-Ala-Sec-Sec-Gly-Ala-Sec-Gly-Ala-Ala-Gly-Cys-Cys-Ala-Cys-Ala
    #
    # ===================================================================== #
    when /^1to3$/i
      e Bioroebe.one_to_three(a?)
    # ===================================================================== #
    # === set_aminoacids
    # ===================================================================== #
    when 'set_aminoacids',
         'aa_seq',
         'aaseq',
         'setaminoacids',
         'setaa',
         'set_aminoacid',
         'set_aa',
         'setamino',
         'setaminoacid',
         'set_aminoacid_sequence'
      set_aminoacids(a?)
    # ===================================================================== #
    # === stop_codons?
    # ===================================================================== #
    when 'stop_codons?',
         /^stopcodons\??$/,
         'scodons?',
         'look_for_stop_codons_in_the_main_sequence',
         /^report(_|-)?all(_|-)?stop(_|-)?codons$/
      report_all_stop_codons
    # ===================================================================== #
    # === version?
    # ===================================================================== #
    when 'version?',
         'version',
         /^feedback(_|-)?version$/i
      feedback_version
    # ===================================================================== #
    # === CpG?
    # ===================================================================== #
    when /^show(_|-)?cpg(_|-)?islands$/,
         'cg?','CG?','CpG?','CpG',
         'cpg?','cpg','cpg_islands',
         'CPG'
      show_cpg_islands
    # ===================================================================== #
    # === is_on_roebe?
    # ===================================================================== #
    when 'is_on_roebe?'
      erev 'Are we on roebe? '+
           verbose_truth(::Bioroebe.is_on_roebe?.to_s)
    # ===================================================================== #
    # === enable_colours
    # ===================================================================== #
    when 'col',
         'enable_colours',
         'enablecolours',
         'ecolours'
      enable_colours
    # ===================================================================== #
    # === enable_colours_in_an_extended_manner
    # ===================================================================== #
    when /enable(_|-| )?colours(_|-| )?in(_|-| )?an(_|-| )?extended(_|-| )?manner$/
      enable_colours_in_an_extended_manner(:be_verbose)
    # ===================================================================== #
    # === deduce_aa_seq?
    #
    # This entry point will show the possible codons that could code for
    # the given aminoacid at hand.
    #
    # Invocation examples:
    #
    #   deduce_this_aminoacid_sequence AARGLKKKLKLMMAAAAA
    #   deduce MTTAGP
    #   deduce MTTAGKLIIBRRSAAP
    #
    # ===================================================================== #
    when /^deduce(_|-| )?this(_|-| )?aminoacid(_|-| )?sequence$/i,
         'deduce',
         'ded',
         'codons',
         'sof',
         'deduce_aa_seq?',
         'sequence_of',
         'sequenceof',
         'peptide',
         'deduce?',
         /^reverse_?DNA$/i,
         /^revseq$/i
      deduce_this_aminoacid_sequence(f)
    # ===================================================================== #
    # === report_main_sequence
    # ===================================================================== #
    when /^report(_|-)?main(_|-)?sequence$/i,
         'report2'
      report_main_sequence
    # ===================================================================== #
    # === stopcodon?
    # ===================================================================== #
    when /^stop_?codon\??/,
         /^determine_?and_?report_?all_?stop_?codons/
      determine_and_report_all_stop_codons
    # ===================================================================== #
    # === what_sequence_is_this?
    # ===================================================================== #
    when 'what_sequence_is_this?',
         'whatsequenceisthis?',
         'whatsequence'
      what_sequence_is_this?
    # ===================================================================== #
    # === tb1
    #
    # This entry point will start the gtk-controller (some gtk-widgets).
    # ===================================================================== #
    when /^tb1$/i
      remote_URL =
        'https://raw.githubusercontent.com/vsbuffalo/bds-files/master/chapter-03-remedial-unix/tb1-protein.fasta'
      cd log_dir?
      esystem 'wget '+remote_URL
      e 'Downloaded into '+sdir(return_pwd)+'.'
    # ===================================================================== #
    # === add_to_start
    # ===================================================================== #
    when /^add(_|-)?start$/i,
         /^add(_|-)?to(_|-)?start$/i,
         'prepend'
        add_to_start(a?)
    # ===================================================================== #
    # === cd                                                       (cd tag)
    #
    # Usage example:
    #
    #   cd /tmp
    #
    # ===================================================================== #
    when 'cd'
      cd(f)
    # ===================================================================== #
    # === blosum62
    # ===================================================================== #
    when /^-?-?blosum62/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === add_polyA
    # ===================================================================== #
    when 'add_poly_a','add_polyA','polya',
         'addpolya',
         '+polyA',
         'polyA'
      e 'Appending a PolyA sequence to the RNA next (onto @rna).'
      add_poly_a_sequence
    # ===================================================================== #
    # === bioroebe --all_blosum
    # ===================================================================== #
    when /^-?-?all(_|-| )?blosum/i # Show all blosum values here.
      array_all_blosums = %w(
        45 50 62 80 90
      ).map {|entry| entry = entry.dup; entry.prepend('blosum') }
      menu(array_all_blosums)
    # ===================================================================== #
    # === blosum45
    # ===================================================================== #
    when /^-?-?blosum45/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === blosum50
    # ===================================================================== #
    when /^-?-?blosum50/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === gc_content?
    #
    # This entry point will calculate the GC content, as a percentage,
    # of the given input sequence. If no input is given then the
    # default DNA sequence will be used (if assigned).
    #
    # Usage example:
    #
    #   GC? ATGGGGGCGCG
    #
    # ===================================================================== #
    when /^gc_?content\??$/i,
         'calculate',
         'cgc',
         'gcontent',
         'gccc',
         /^GC\??$/i,
         'gccontent?',
         'gc_percent',
         'gcpercent'
      calculcate_gc_content(a?) # This variant will be verbose.
    # ===================================================================== #
    # === www_finder
    #
    # Invocation example:
    #
    #   bioroebe --gtk-www-finder
    #
    # ===================================================================== #
    when 'www_finder',
         'wwwfinder',
         'wfind',
         'wfinder',
         /^-?-?gtk(_|-| )?www(_|-| )?finder$/i
      load_gtk
      require 'bioroebe/gui/gtk3/www_finder/www_finder.rb'
      e 'Starting the WWWFinder next.'
      thread = Thread.new { Bioroebe::GUI::Gtk::WwwFinder.run_gtk3_widget }
      thread.join
    # ===================================================================== #
    # === bioroebe --gtk-levensthein
    # ===================================================================== #
    when /^-?-?gtk(_|-| )?levensthein$/i,
         /^-?-?levensthein(_|-| )?gui$/i
      require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
      Bioroebe::GUI::Gtk::LevenstheinDistance.run
    # ===================================================================== #
    # === count_aminoacids
    # ===================================================================== #
    when 'count_aminoacids',
         'countaminoacids',
         'caminoacids',
         'aminoacid_composition',
         'aminoacidcomposition',
         'acomposition'
      count_amount_of_aminoacids(f)
    # ===================================================================== #
    # === 3iyq.pdb
    # ===================================================================== #
    when '3iyq.pdb'
      download(
        'https://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=fastachain&compression=NO&structureId=3IYR&chainId=B'
      )
    # ===================================================================== #
    # === ubiquitin?
    #
    # This method will simply show the default ubiquitin-sequence.
    # ===================================================================== #
    when 'ubuiquitin?',
         'ubiquitin?',
         'u?',
         'ubiquitin',
         'ub?',
         'return_ubiquitin_sequence',
         'ubi?'
      erev 'N-Terminus '+steelblue(
             ::Bioroebe.return_ubiquitin_sequence
           )+rev+' C-Terminus'
    # ===================================================================== #
    # === KDEL?
    #
    # This entry point will search for a KDEL sequence in the
    # corresponding amino acid sequence.
    #
    # How to test this:
    #
    #   assign AAAAAATTTGGGCCCGCGCCCTTTAAAGATGAACTA; KDEL?
    #
    # ===================================================================== #
    when 'KDEL?',
         'KDEL',
         'find_kdel_sequence'
      find_kdel_sequence
    # ===================================================================== #
    # === bioroebe --blosum80
    # ===================================================================== #
    when /^-?-?blosum80/i
      e 'Showing '+i.delete('-')+' next.'+N+N
      Bioroebe::BlosumParser.show_as_2D_table(i)
    # ===================================================================== #
    # === levensthein
    # ===================================================================== #
    when 'levensthein',
         'lst'
      interactive_use_of_levensthein
    # ===================================================================== #
    # === hamming_distance?
    # ===================================================================== #
    when 'hamming','hamming?',
         /^hamming(_|-| )?distance\??$/,
         /^-?-?hamming$/,
         'the_hamming_distance',
         'align'
      calculate_hamming_distance_of(a?)
    # ===================================================================== #
    # === mass_weight?
    # ===================================================================== #
    when 'mass_weight?',
         'mass_weight',
         'massweight',
         'aa_mass',
         'ma' # Calculate weight of proteins.
      mass_weight(f)
    # ===================================================================== #
    # === show_molweight
    #
    # This entry point will show the molecular weights of the four main
    # DNA bases - Adenin, Guanin, Cytosin and Thymin.
    # ===================================================================== #
    when /^show(_|-)?molweight$/i,
         'molweight?',
         'mweight?',
         'm?'
      show_molweight
    # ===================================================================== #
    # === okular
    # === evince
    #
    # This is mostly so that we can quickly use common .pdf viewers.
    # ===================================================================== #
    when 'okular',
         'evince'
      verbose_handle_this_sys_command(i, a?)
    # ===================================================================== #
    # === RNAfold1
    # ===================================================================== #
    when 'RNAfold1'
      esystem 'RNAfold < test.seq'
    # ===================================================================== #
    # === design_polylinker
    # ===================================================================== #
    when /^design(_|-)?polylinker$/i,
         'polylinker?',
         'mcs',
         'mcs?',
         'primer?'
      e colourize_nucleotide(design_polylinker(f))
    # ===================================================================== #
    # === seqsize2
    # ===================================================================== #
    when /seqsize(\d+)/,
         /seq(\d+?)size\??/ # See: http://rubular.com/r/IDvU2LJBSA for the second regex
      _ = $1.to_s.dup
      case _
      when '2'
        report_size_of_this_sequence seq2?,''
      when '3'
        report_size_of_this_sequence seq3?,''
      when '4'
        report_size_of_this_sequence seq4?,''
      when '5'
        report_size_of_this_sequence seq5?,''
      when '6'
        report_size_of_this_sequence seq6?,''
      end
    # ===================================================================== #
    # === set_locus
    # ===================================================================== #
    when /set_?locus/,
         'locus'
      set_locus(a?) # set_locus NM_021964
    # ===================================================================== #
    # === coding_entry
    #
    # This entry point can be used like this:
    #
    #   coding_entry 51..3251
    #
    # ===================================================================== #
    when /^coding_?entry/
      designate_this_input_as_coding_entry(a?)
    # ===================================================================== #
    # === multiline_fasta
    # ===================================================================== #
    when 'multiline_fasta',
         'multilinefasta',
         'mfasta',
         'm_fasta',
         'multi_assign','multiassign','multifasta',/input_?fasta/
      obtain_multiline_fasta # in fasta.rb
    # ===================================================================== #
    # === prosite
    # ===================================================================== #
    when 'prosite',
         'prosite_homepage'
      e 'PROSITE - a database of protein families and domains.'
      e (_ = Bioroebe.try_to_pass_through_beautiful_url(:prosite))
      open_in_browser _
    # ===================================================================== #
    # === restriction_enzymes_run
    # ===================================================================== #
    when 'test_restriction_enzymes_run','restriction_enzymes_run'
      pp restriction_enzymes_run
    # ===================================================================== #
    # === show_jumper_directories
    # ===================================================================== #
    when 'jumper?','jumpers?','show_jumper_directories',
         'showjumperdirectories'
      show_jumper_directories
    # ===================================================================== #
    # === reset
    # ===================================================================== #
    when 'reset',
         'tabula rasa',
         'tabula_rasa',
         'tabula',
         'clear_aa',
         'cleara',
         'clearaa'
      erev 'Resetting the Bioroebe::Shell now.'
      reset_to_the_initial_state
    # ===================================================================== #
    # === set_highlight_colour
    # ===================================================================== #
    when /^set_?highlight_?colour/,'seek'
      _ = f
      _ = _.to_sym if _
      set_highlight_colour_or_search_for_this_sequence(_)
    # ===================================================================== #
    # === to_DNA
    # ===================================================================== #
    when /^to(_|-| )?DNA/i
      e Bioroebe.to_dna('ACCACACCAUUUCCCAUGGGUGUGUGG') # => "ACCACACCATTTCCCATGGGTGTGTGG"
    # ===================================================================== #
    # === files?
    # ===================================================================== #
    when 'files?',
         'file?',
         'files',
         'feedback_where_files_are_kept_locally',
         'feedbackwherefilesarekeptlocally'
      feedback_where_files_are_kept_locally
    # ===================================================================== #
    # === buffer?
    # ===================================================================== #
    when 'buffer?','b?','show_xorg_buffer2',
         'feedback_whether_we_will_also_set_the_xorg_buffer'
      feedback_whether_we_will_also_set_the_xorg_buffer
      show_xorg_buffer
    # ===================================================================== #
    # === toggle
    # ===================================================================== #
    when 'toggle'
      toggle_xorg_buffer
      buffer?
    # ===================================================================== #
    # === average?
    # ===================================================================== #
    when 'average?',
         'average','avg?',
         'show_average',
         'molecular_weight?','mw', # Perhaps we will move the last entry here.
         /show(_|-)?average(_|-)?weight(_|-)?of(_|-)?a(_|-)?nucleotide$/
      show_average_weight_of_an_aminoacid
      show_average_weight_of_a_nucleotide
    # ===================================================================== #
    # === test
    # ===================================================================== #
    when /test/
      e 'THIS IS A TEST.'
    # ===================================================================== #
    # === sigma?
    # ===================================================================== #
    when 'sigma_tutorial',
         'sigma?',
         'sigmatutorial',
         'sig?',
         'stutorial'
      show_sigma_tutorial
    # ===================================================================== #
    # === stop?
    # ===================================================================== #
    when /^stop\??$/i,
         'BLA',
         'end?'
      if dna_sequence?.empty?
        e 'Please first assign a sequence.'
      else
        e
        report_main_sequence(:stop_codon)
        e
      end
    # ===================================================================== #
    # === mode?
    # ===================================================================== #
    when 'mode?',
         /^report(_|-)?mode$/i
      report_mode
    # ===================================================================== #
    # === todo?
    # ===================================================================== #
    when 'todo?'
      _ = 'https://www.biostars.org/'
      show_todo_file
      erev 'Also consider visiting: '
      e
      erev "  #{_}"
      e
      set_xclip _
    # ===================================================================== #
    # === numbered?
    # ===================================================================== #
    when /^numbered\??/,
         /^with(_|-)?numbers$/i,
         /^show(_|-)?numbered(_|-)?nucleotide(_|-)?positions$/i
      show_numbered_nucleotide_positions
    # ===================================================================== #
    # === padding?
    # ===================================================================== #
    when 'padding?'
      pp padding?
    # ===================================================================== #
    # === Handle +3 and similar instructions
    # ===================================================================== #
    when /^\+(\d+)/ # See http://rubular.com/r/JaeO91V1vt
      add_n_nucleotides($1)
    # ===================================================================== #
    # === highlight
    # ===================================================================== #
    when /^highlight/,'high' # ← This variant is always verbose.
      set_highlight_colour(f, :be_verbose)
    # ===================================================================== #
    # === show_all_codon_tables
    # ===================================================================== #
    when 'show_all_codon_tables',
         'all_codon_tables',
         'atables',
         'alltable?',
         'showallcodontables',
         'codons?',
         'codontables',
         'codontables?',
         'show3',
         'showtables',
         'show_codon_tables'
      show_all_codon_tables
    # ===================================================================== #
    # === seq3?
    # ===================================================================== #
    when 'seq3?','s3?'
      show_seq_3
    # ===================================================================== #
    # === seq4?
    # ===================================================================== #
    when 'seq4?','s4?'
      show_seq_4
    # ===================================================================== #
    # === seq5?
    # ===================================================================== #
    when 'seq5?','s5?'
      show_seq_5
    # ===================================================================== #
    # === seq6?
    # ===================================================================== #
    when 'seq6?','s6?'
      show_seq_6
    # ===================================================================== #
    # === do_analyze_protein_sequence
    # ===================================================================== #
    when 'do_analyze_protein_sequence','do_analyze_sequence',
         'doanalyzesequence','analyze_sequence','analyzesequence'
      do_analyze_sequence
    # ===================================================================== #
    # === glycolysis?
    # ===================================================================== #
    when 'glycolysis?',
         'glykolyse?',
         'glykolyse',
         'glycolysis',
         'glykolysis',
         'display_glycolysis_pathway',
         'glyk?',
         'glyc?'
      display_glycolysis_pathway
    # ===================================================================== #
    # === result?
    # ===================================================================== #
    when 'result?'
      e @internal_hash[:result]
    # ===================================================================== #
    # === cysteines?
    #
    # This entry point will quickly show all cysteines in the given
    # aminoacid sequence. This is meant mostly as a visual aid to
    # the user on the commandline.
    # ===================================================================== #
    when /^-?-?cysteines\??$/i
      _ = aminoacid_sequence? # Get our aminoacid sequence first.
      erev _.to_s.gsub(/C/, gold('C')+rev)
    # ===================================================================== #
    # === Handle -3 and similar instructions
    # ===================================================================== #
    when /^\-(\d+)/
      remove_n_nucleotides($1)
    # ===================================================================== #
    # === pad
    # ===================================================================== #
    when 'pad'
      e pad?+f.to_s
    # ===================================================================== #
    # === ori?
    # ===================================================================== #
    when 'ori?',
         'show_ori_sequences',
         'showorisequences'
      show_ori_sequences
    # ===================================================================== #
    # === short_aa
    # ===================================================================== #
    when 'short_aa',
         'shortaa',
         'shorten_aa'
      dna_to_aminoacid_sequence(a?)
    # ===================================================================== #
    # === add_his_tag
    # ===================================================================== #
    when /add(_|-)?his(_|-)?tag/
      add_his_tag('add 6 random his tags') 
    # ===================================================================== #
    # === names? 
    # ===================================================================== #
    when 'names?'
      show_how_to_use_the_names_for_the_taxonomy_table
    # ===================================================================== #
    # === gem?
    # ===================================================================== #
    when 'gem?','rubygem?',
         /^bioroebe(_|-)?gem/
      remote_URL = 'https://rubygems.org/gems/bioroebe'
      e remote_URL
      open_in_browser(remote_URL) if is_on_roebe?
    # ===================================================================== #
    # === set_download_folder
    # ===================================================================== #
    when /^set(_|-)?download(_|-)?folder$/i,
         'set_download_directory',
         'setdownloaddirectory',
         'setdir'
      set_download_directory(f)
    # ===================================================================== #
    # === parse_taxonomy
    # ===================================================================== #
    when /^parse_?taxonomy/,
         'ptaxo',
         'ptax'
      ParseTaxonomy.new(a?)
    # ===================================================================== #
    # === bisulfite
    #
    # Apply a bisulfite-run against the current sequence at hand.
    #
    # Usage examples:
    #
    #   bisulfite CCCGCAATGCATACCTCGCCG
    #   bis CCCGCAATGCATACCTCGCCG
    #
    # ===================================================================== #
    when /^bisulfite$/,
         /^bis$/
      e format_this_nucleotide_sequence(
          bisulfite(a?)
        )
    # ===================================================================== #
    # === longest_substring?
    #
    # Usage example:
    #
    #   longest_substring? ATGGGAAT GGG
    #
    # ===================================================================== #
    when /^longest(_|-)?substring\??$/,
         /^LCS$/i,
         'McIlroy-Hunt algorithm'
      find_longest_substring_via_LCS(a?)
    # ===================================================================== #
    # === yaml_engine?
    # ===================================================================== #
    when /^yaml(_|-)?engine\??$/i,
         /^report(_|-)?which(_|-)?yaml(_|-)?engine(_|-)?is(_|-)?in(_|-)?use$/, # === report_which_yaml_engine_is_in_use
         /^syck\??$/i
      report_which_yaml_engine_is_in_use
    # ===================================================================== #
    # === ecoli
    # ===================================================================== #
    when /ecoli\??/
      erev '  https://ecocyc.org/'
    # ===================================================================== #
    # === selenocysteine
    # ===================================================================== #
    when /selenocysteine\??/
      erev 'UGA codes for selenocysteine.'
    # ===================================================================== #
    # === aa_analyze?
    # ===================================================================== #
    when 'aa_analyze?',
         'aa_analyze',
         'aminoacid_sequence?',
         /aminoacidsequence\??/,
         'aminoacid_analyze',
         'aminoacidanalyze',
         'protein_composition?',
         'asequence',
         'asequence?'
      show_protein_composition(aminoacid_sequence?)
      molecular_mass_of_amino_acids_in_this_sequence(aminoacid_sequence?)
    # ===================================================================== #
    # === find_TATA
    # ===================================================================== #
    when 'tata?','tata','TATA?',
         /^find(_|-)?TATA\??$/
      search_for_tata_consensus_sequence
    # ===================================================================== #
    # === restore_prompt
    # ===================================================================== #
    when /^restore(_|-)?prompt$/i,
         /^restore(_|-)?default(_|-)?prompt$/i
      restore_default_prompt
    # ===================================================================== #
    # === BASE_DIR
    # ===================================================================== #
    when /^BASE(_|-)?DIR$/i
      e sdir(Bioroebe.base_directory?)
    # ===================================================================== #
    # === histone_table?
    # ===================================================================== #
    when 'histone_table?','htable','show_histone_table','showhistonetable'
      show_histone_table
    # ===================================================================== #
    # === primer
    # ===================================================================== #
    when 'primer'
      primer(f)
    # ===================================================================== #
    # === GFF
    # ===================================================================== #
    when /^GFF\??$/i
      show_information_about_the_gff_format
    # ===================================================================== #
    # === frame1
    # ===================================================================== #
    when 'frame1',
         'f1',
         'f'
      showorf(dna_sequence?, :frame1)
    # ===================================================================== #
    # === open_in_browser
    #
    # Usage example:
    #
    #   oib https://www.uniprot.org/uniprot/P62897
    #
    # ===================================================================== #
    when /^open(_|-)?in(_|-)?browser$/i,
         'oib'
      open_in_browser(a?)
    # ===================================================================== #
    # === composition?
    #
    # This entry point will show the composition of the given DNA sequence
    # at hand.
    # ===================================================================== #
    when /^show(_|-)?composition$/,
         'composition?',
         'composition',
         'comp',
         'compo',
         'compo?',
         'comp?',
         'scompo'
      show_composition
    # ===================================================================== #
    # === load
    # ===================================================================== #
    when 'load',
         /^load(_|-)?from$/i,
         /^use$/i
      load(a?)
    # ===================================================================== #
    # === load_dna
    # ===================================================================== #
    when /^load(_|-)?dna$/i
      load_dna
    # ===================================================================== #
    # === transeq
    # ===================================================================== #
    when 'transeq','transseq','teq'
      i = a?
      i = dna_sequence? unless i
      if i.is_a?(Array) and i.empty?
        i = dna_sequence?
      end
      ::Bioroebe::DnaToAminoacidSequence.new(i) { :be_verbose } # bl dna/dna_to_aminoacid_sequence.rb
    # ===================================================================== #
    # === display_open_reading_frames
    #
    # Usage example:
    #
    #   display_open_reading_frames ATGAGCAAGGCCGACTACGAGAAG
    #
    # ===================================================================== #
    when /^display(_|-)?open(_|-)?reading(_|-)?frames$/i
      display_open_reading_frames(a?) { :show_three_frames }
    # ===================================================================== #
    # === ruler-no-colours
    # ===================================================================== #
    when /^-?-?ruler(_|-)?no(_|-)?colours?$/,
         'ruler2'
      show_sequence_with_a_ruler(first_argument?) { :without_colours }
    # ===================================================================== #
    # === reverse
    # ===================================================================== #
    when 'reverse',
         /^reverse(_|-)?sequence$/,
         'reverse_seq' # This will reverse the complement.
      show_reverse_dna_string
    # ===================================================================== #
    # === reverse!
    # ===================================================================== #
    when 'reverse!'
      set_dna_sequence(return_reverse_dna_string)
    # ===================================================================== #
    # === aasize
    # ===================================================================== #
    when 'aasize',
         'asize',
         'aasize?',
         'aa_size?',
         /^report(_|-)?aminoacid(_|-)?size$/i,
         'reportaasize'
      report_how_many_aminoacids_we_have
    # ===================================================================== #
    # === base_composition
    #
    # Use this like so:
    #
    #    base_composition 10 20 30 40
    #    base_composition 5 5 5 85
    #
    # ===================================================================== #
    when /base_composition/
      hash = {}
      hash[:A] = 0
      hash[:T] = 0
      hash[:C] = 0
      hash[:G] = 0
      hash[:A] = a?[0].to_i
      hash[:T] = a?[1].to_i
      hash[:C] = a?[2].to_i
      hash[:G] = a?[3].to_i
      display_this_sequence(
        Bioroebe.generate_random_dna_sequence(
          :default,
          hash
        )
      )
    # ===================================================================== #
    # === shuffle
    # ===================================================================== #
    when 'shuffle',
         'do_shuffle',
         /^shuffle(_|-)?main(_|-)?string$/i
      shuffle_main_string
    # ===================================================================== #
    # === allweights?
    # ===================================================================== #
    when 'allweights?',
         'allweight',
         'all_weight',
         'allweights',
         'gewicht'
      %w( A T C G U ).each {|entry|
        show_weight_of_this_nucleotide(entry)
      }
    # ===================================================================== #
    # === default
    # ===================================================================== #
    when 'default','def','d' # default action to use.
      i = 'shorten Lys Ser Pro Ser Leu Asn Ala Ala Lys'
      check_input_against_case_menu
    # ===================================================================== #
    # === upcase
    # ===================================================================== #
    when 'upcase',
         'ucase',
         'upcase_main_string',
         'upcasemainstring',
         'uppercase',
         'to_upper',
         'upcas'
      upcase_main_string
    # ===================================================================== #
    # === weight_of_common_proteins?
    #
    # This entry point allows us to show the weight of some common
    # problems, e. g. for easy commandline-display.
    # ===================================================================== #
    when /^weight(_|-)?of(_|-)?common(_|-)?proteins\??/,
         /^show(_|-)?the(_|-)?weight(_|-)?of(_|-)?some(_|-)?common(_|-)?proteins/,
         /^protein(_|-)?mass\??/,
         /^table(_|-)?weights$/i,
         /^weight(_|-)?table$/i,
         'molecular_weights?',
         'sizes?',
         'weights',
         'massweights',
         'molweights?',
         'masssize',
         'showweights',
         'proteins?'
      show_the_weight_of_some_common_proteins
    # ===================================================================== #
    # === protein_weight?
    # ===================================================================== #
    when /^protein(_|-)?weight\??/i,
         /^report(_|-)?the(_|-)?protein(_|-)?weight$/i
      report_the_protein_weight
    # ===================================================================== #
    # === show_weight_of_this_nucleotide
    # ===================================================================== #
    when 'show_weight_of_this_nucleotide',
         'molweight',
         'showweightofthisnucleotide'
      show_weight_of_this_nucleotide(f)
    # ===================================================================== #
    # === weights?
    # ===================================================================== #
    when 'weights?'
      MolecularWeightOfNucleotides.report_weight
    # ===================================================================== #
    # === controller
    #
    # This entry point will start the gtk-controller (some gtk-widgets).
    #
    # Invocation example:
    #
    #   bioroebe --gui
    #
    # ===================================================================== #
    when /^-?-?controller$/i,
         /^-?-?gui$/i,
         /^-?-?gtk(_|-| )?notebook$/i,   # === bioroebe --gtk-notebook
         /^-?-?gtk(_|-| )?controller$/i,
         /^-?-?notebook$/i
      start_gtk_controller
      # =================================================================== #
      # === download                                   (download tag, dl tag)
      #
      # Generic download-related entry point. This can be used like in
      # the following way:
      #
      #   download lambda
      #
      # =================================================================== #
      when /^download$/i
        download(a?)
      # =================================================================== #
      # === download?
      # =================================================================== #
      when 'download?',
           'show_last_downloaded_file',
           'showlastdownloadedfile'
        show_last_downloaded_file
      # =================================================================== #
      # === test
      # =================================================================== #
      when 'test' # Throwaway method for testing.
        # @bioroebe.lazy
        set_dna_sequence '
          ATGTCTGGGGACGCTCCCGATCGGCTCCCGTAACTTACACGGTCTACACAAGACGTGTGTGTATGTCGTCGGACCTTTTAGCTATGAGGCTCGAATGAAGCTACCGAGCCATATCTACGCAGCCTTTTATGGGAACATCAGCATATTTCAATCTACCGCCAGGATGTTGATCCCCGGATGTTAAGGGTTAACCAGTATGATGAACATGGAATTGTGAAGTTACTACGGTTCATTCACGGACGACGCCAAGTTACCATTCTTGCTAACTATCGTCCAGGGATTTTGATATGCATCTGCTCACCTCTGTAGCGGCCTCCCGGAGCTGTCACCACAATC
        '
        e sienna(dna_seq?)
        find_all_orfs
      # =================================================================== #
      # === tphages?
      # =================================================================== #
      when 't-phages?',
         'tphages?',
         /^show(_|-)?t(_|-)?phages$/,
         'tphages',
         'tt','phages?'
      show_t_phages
      # =================================================================== #
      # === raw_sequence?
      # =================================================================== #
      when /^-?-?raw(_|-| )?sequence\??$/i,
           /^-?-?raw(_|-| )?conversion\??$/i
        e sfancy(leading_five_prime)+
          colourize_nucleotide_sequence(
            raw_sequence?, :make_no_modifications
          )+
          sfancy(trailing_three_prime)
    # ===================================================================== #
    # === perform_startup_actions
    # ===================================================================== #
    when /^perform(_|-)?startup(_|-)?actions$/,
         /^startup(_|-)?actions$/
      perform_startup_actions
    # ===================================================================== #
    # === to_fasta
    #
    # toasta is an alias to this entry point.
    # ===================================================================== #
    when /^to(_|-)?f?asta$/i
      to_fasta
    # ===================================================================== #
    # === cat
    # ===================================================================== #
    when 'cat',
         'show_the_content_of_this_file'
      cat(f) # Show the content of a file.
    # ===================================================================== #
    # === blosum?
    # ===================================================================== #
    when 'blosum?',
         'blosum',
         'blosu',
         'blos',
         'blo',
         'bl',
         'b',
         'show_blosum_matrix',
         'matrix',
         'losum'
      show_blosum_matrix
    # ===================================================================== #
    # === debug?
    # ===================================================================== #
    when 'debug?'
      feedback_whether_we_are_in_debug_mode
    # ===================================================================== #
    # === protein_stats?
    # ===================================================================== #
    when 'protein_stats?',
         'protein_stats',
         'pstats?',
         'pstats'
      protein_stats
    # ===================================================================== #
    # === digest
    # ===================================================================== #
    when 'digest',
         /^digest(_|-)?at$/i,
         /^cut(_|-)?with$/i,
         /^cut(_|-)?to$/i
      digest(a?)
    # ===================================================================== #
    # === amino_acids_frequency?
    # ===================================================================== #
    when /^amino(_|-)?acids(_|-)?frequency\??$/i,
         /^show(_|-)?the(_|-)?amino(_|-)?acids(_|-)?frequencies$/i,
         'aa_frequency?',
         'aafrequency?'
      show_the_aminoacids_frequencies
    # ===================================================================== #
    # === basedir?
    # ===================================================================== #
    when /basedir\??/,
         'dir?',
         'base_dir?',
         'log_dir',
         'log_dir?'
      show_config_dir
      show_save_file
      show_log_dir
    # ===================================================================== #
    # === show_log_dir
    # ===================================================================== #
    when /^show(_|-)?log(_|-)?dir$/,
         'logdir?',
         'logdir',
         'sdir?',
         'slog',
         'log?',
         /^-?-?location\??$/i,
         'localdir?'
      show_log_dir
    # ===================================================================== #
    # === set_log_dir
    #
    # This entry point can be used to set a specific log directory
    # from within a running instance of the bioshell.
    #
    # Invocation examples:
    #
    #   set_log_dir /tmp/test
    #   setlogdir /tmp/test
    #
    # ===================================================================== #
    when /^set(_|-)?log(_|-)?dir$/i
      set_log_dir(first_argument?) { :be_verbose }
    # ===================================================================== #
    # === chunked_display
    #
    # Usage example:
    #
    #   cdisplay ATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACACATGACAGGACACACTTTTAGCACACAC
    #
    # ===================================================================== #
    when /^chunked(_|-)?display$/i,
         'properly_number','cdisplay',
         'chunked',
         'chunk',
         /^beautify(_|-)?body$/
      chunked_display(a?)
    # ===================================================================== #
    # === *
    # ===================================================================== #
    when '*'
      erev 'The occurrence of * in a amino acid sequence denotes a STOP codon.'
    # ===================================================================== #
    # == mmass
    #
    # Usage example:
    #
    #   molmass Glycine
    #
    # ===================================================================== #
    when 'mmasse',
         'molecular_mass_of',
         'molecularmassof',
         'mmase',
         'masse?',
         'molmasse',
         'molmass'
      molecular_mass_of(f)
    # ===================================================================== #
    # === showorf
    # ===================================================================== #
    when /^showorfs?$/,
         'showor',
         'show_orf',
         'show_the_orf'
      showorf(a?)
    # ===================================================================== #
    # === bioshell --permanently-disable-startup-intro
    # ===================================================================== #
    when /^-?-?permanently(_|-)?disable(_|-)?startup(_|-)?intro$/
      permanently_disable_startup_intro
    # ===================================================================== #
    # === startup_info?
    #
    # This entry point exists mostly as a debug-aid.
    # ===================================================================== #
    when /^-?-?startup(_|-)?info\??$/i,
         /^-?-?show(_|-)?startup(_|-)?information$/i,
         /^-?-?show(_|-)?intro$/i,
         /^-?-?sintro$/
      show_startup_information
    # ===================================================================== #
    # === downcase_main_string
    # ===================================================================== #
    when /^downcase(-|_| )?main(-|_| )?string$/,
         /^downcase$/i,
         'dcase',
         'down',
         'lower'
      downcase_main_string
    # ===================================================================== #
    # === silent-startups
    # ===================================================================== #
    when /^-?-?silent(-|_)?startup$/,
         /^-?-?silent$/
      do_a_silent_startup
    # ===================================================================== #
    # === seqsize?
    # ===================================================================== #
    when 'seqsize?'
      e sequence?.to_s.size
    # ===================================================================== #
    # === alu?
    # ===================================================================== #
    when 'alu?',
         'show_alu_sequence',
         'alu_sequence?'
      show_alu_sequence
    # ===================================================================== #
    # === positions?
    # ===================================================================== #
    when 'positions?','positions',
         'show_positions','showpositions',
         'show_position_of_sequence','showpositionofsequence',
         'pos?'
      show_position_of_sequence
    # ===================================================================== #
    # === codon_usage_analyzer
    # ===================================================================== #
    when /^codon_?usage_?analyzer/
      ShowCodonUsage.new(dna_string?)
    # ===================================================================== #
    # === return_all_genes
    # ===================================================================== #
    when 'return_all_genes',
         'returnallgenes'
      return_all_genes
    # ===================================================================== #
    # === install
    # ===================================================================== #
    when 'install'
      install(f)
    # ===================================================================== #
    # === enable
    # ===================================================================== #
    when 'enable',
         'use'
      enable(a?)
    # ===================================================================== #
    # === do_use_expand_cd_aliases
    # ===================================================================== #
    when 'do_use_expand_cd_aliases',
         'douseexpandcdaliases',
         'cdaliases',
         /use(_|-)?expanded(_|-)?aliases$/i # === use_expanded_aliases
      enable :cd_aliases
    # ===================================================================== #
    # === do_not_use_expand_cd_aliases
    # ===================================================================== #
    when 'do_not_use_expand_cd_aliases',
         'no_expand_cd_aliases',
         'no_cd_aliases'
      disable :cd_aliases
    # ===================================================================== #
    # === use_expand_cd_aliases?
    # ===================================================================== #
    when /^use(_|-)?expand(_|-)?cd(_|-)?aliases\??$/i,
         '@use_expand_cd_aliases',
         /^report(_|-)?whether(_|-)?we(_|-)?will(_|-)?make(_|-)?use(_|-)?of(_|-)?expand(_|-)?cd(_|-)?aliases$/i
      report_whether_we_will_make_use_of_expand_cd_aliases
    # ===================================================================== #
    # === pir
    # ===================================================================== #
    when 'pir?',
         'pir'
      e "  #{Bioroebe.try_to_pass_through_beautiful_url('pir').first}"
    # ===================================================================== #
    # === chromosome_table
    # ===================================================================== #
    when /^chromosome(_|-)?table$/i,
         /^show(_|-)?chromosome(_|-)?table$/i
      show_chromosome_table
    # ===================================================================== #
    # === findgene?
    # ===================================================================== #
    when 'findgene?',
         'notify_the_user_as_to_how_findgene_works'
      notify_the_user_as_to_how_findgene_works
    # ===================================================================== #
    # === calculate_exponential_growth
    #
    # Invocation example:
    #
    #   calculate_exponential_growth 1, 10
    #
    # ===================================================================== #
    when /calculate(_|-)?exponential(_|-)?growth$/
      calculate_exponential_growth(first_argument, second_argument)
    # ===================================================================== #
    # === test_help
    # ===================================================================== #
    when 'test_help','testhelp','new_help','newhelp','1'
      ::Bioroebe::Shell::Help[]
    # ===================================================================== #
    # === fasta1
    #
    # This entry point allows us to quickly refer to different
    # FASTA entries from a file, such as:
    #
    #   fasta5 # refers to the 5th entry
    #   fasta6 # refers to the 6th entry
    #   ^^^ and so forth
    #
    # ===================================================================== #
    when /^fasta(\d{1,10})$/i
      try_to_display_this_fasta_entry($1.to_s.dup) { :and_assign_it_as_well }
    # ===================================================================== #
    # === will_we_truncate?
    # ===================================================================== #
    when 'truncate?',
         'will_we_truncate?'
      will_we_truncate?
    # ===================================================================== #
    # === When it starts with one or more numbers, including a ' '.
    #     Example: 100 aa
    # ===================================================================== #
    when /^\d+ aa/ # See: http://rubular.com/r/Lnf2b9RTGP
      case f
      when 'aa'
        create_n_random_amino_acids(_)
      end
    # ===================================================================== #
    # === append_aminoacid
    # ===================================================================== #
    when 'append_aminoacid',
         'add_aa',
         'addaa',
         'append_aa' # Append to aa.
      @internal_hash[:aminoacids] << a
    # ===================================================================== #
    # === find_nls
    # ===================================================================== #
    when 'find_nls',
         'nls',
         'nls_finder',
         'nlsfinder',
         'run_nls_search'
      run_nls_search
    # ===================================================================== #
    # === GFP?
    # ===================================================================== #
    when 'GFP?',
         /^show_?GFP_?sequence$/i,
         /^gfp\??/
      erev "The #{rosybrown('GFP sequence')}#{rev} is:#{N}#{N}"
      show_GFP_sequence
      e
      erev 'Note: If you wish to assign this as the new main nucleotide'
      erev 'sequence, then use this command:'
      e
      erev '  '+sfancy('  assign :GFP')
      e
    # ===================================================================== #
    # === colourize_fasta
    # ===================================================================== #
    when 'colourize_fasta',
         'colourizefasta',
         'colourize_fasta_file',
         'colourizefastafile'
      colourize_fasta_file(a?)
    # ===================================================================== #
    # === urls?
    # ===================================================================== #
    when 'urls?',
         'url?'
      e 'Showing some URLs next:'
      e
      erev '  ftp://ftp.ncbi.nih.gov/genbank/'
      erev '  https://rosalind.info/problems/list-view/'
      erev '  https://biotools.umassmed.edu/bioapps/primer3_www.cgi # Primerdesign'
      e
      pdb_url? # And also show the PDB Url.
    # ===================================================================== #
    # === loxp?
    # ===================================================================== #
    when 'loxp?',
         'loxp'
      erev 'Next showing the loxP sequence:'
      _ = 'ATAACTTCGTATA'
      e
      e sfancy(_)
      e
      find_this_sequence(_) unless dna_sequence?.empty?
    # ===================================================================== #
    # === blast
    # ===================================================================== #
    when 'blast'
      open_blast_webpage
    # ===================================================================== #
    # === telomer?
    # ===================================================================== #
    when 'telomer?',
         'telomere?'
      e padding?+leading_five_prime+'TTAGGG'+trailing_three_prime
    # ===================================================================== #
    # === save_my_file
    # ===================================================================== #
    when /^save(_|-)?my(_|-)?file$/,
         'save'
      save_my_file { :be_verbose }
    # ===================================================================== #
    # === rev?
    # ===================================================================== #
    when 'rev?'
      e 'Testing rev next, the ability to revert to the default colour.'
      pp ::Bioroebe.rev
      if ::Bioroebe.rev.empty?
        e 'Not using any special colours presently.'
      else
        e 'Using special colours.'
      end
      e "Red then revert, if colours are enabled: "\
        "#{swarn('Red then')}#{rev} revert."
    # ===================================================================== #
    # === available_colours?
    # ===================================================================== #
    when /^available_?colours\??/,
         /^show_?html_?colours/,
         'highlight?'
      show_html_colours
    # ===================================================================== #
    # === seq_with_tab?
    # ===================================================================== #
    when /seq_?with_?tab\??/,
         'splitted',
         'splitter'
      show_string { :with_colourized_separator }
    # ===================================================================== #
    # === barrier
    # ===================================================================== #
    when 'barrier','vertical','verti',
         /^add(_|-)?vertical(_|-)?barrier(_|-)?to(_|-)?sequence$/
      add_vertical_barrier_to_sequence(a?)
    # ===================================================================== #
    # === seq5
    # ===================================================================== #
    when /seq5/
      @internal_hash[:array_sequences[4]] = only_valid_dna_nucleotides(a?)
    # ===================================================================== #
    # === pdf_tutorial
    # ===================================================================== #
    when 'generate_pdf_tutorial',
         'generatepdftutorial',
         'generate_pdf_documentation',
         'gpdf',
         'pdf_tutorial',
         'create_pdf'
      erev 'Next creating a .pdf file that includes the Tutorial.'
      generate_pdf_tutorial
    # ===================================================================== #
    # === GenbankFlatFileFormatGenerator
    # ===================================================================== #
    when /^Genbank_?Flat_?File_?Format_?Generator/i
      if File.exist? f
        object = GenbankFlatFileFormatGenerator.new(f)
        pp object
      else
        no_file_exists_at(f)
      end
    # ===================================================================== #
    # === bla
    # ===================================================================== #
    when 'bla' # This is just a test.
      e Bioroebe.store_here?
      e Bioroebe.log_dir
    # ===================================================================== #
    # === debug_seq?
    # ===================================================================== #
    when 'debug_seq?'
      pp string? # Show in a "debug" variant.
    # ===================================================================== #
    # === lernen
    # ===================================================================== #
    when 'lernen'
      _ = 'https://www.biostars.org/'
      e 'Now opening '+_
      open_in_browser(_)
    # ===================================================================== #
    # === peroxisome_pts1
    # ===================================================================== #
    when 'peroxisome_pts1'
      erev '-Ser-Lys-Leu-COOH'
    # ===================================================================== #
    # === atp_cost?
    #
    # Usage example:
    #
    #   atp_cost? 2
    #
    # ===================================================================== #
    when 'atp_cost?',
         'atpcost?',
         'atpcost',
         'atp?'
      calculate_atp_cost_for(a?)
    # ===================================================================== #
    # === vectors?
    # ===================================================================== #
    when /^-?-?vectors\??/,
         /^-?-?show_?available_?vectors?/,
         /^-?-?show_?vector/
      show_available_vectors # show_available_vectors
    # ===================================================================== #
    # === seq3
    # ===================================================================== #
    when /seq3/
      @internal_hash[:array_sequences[2]] = only_valid_dna_nucleotides(a?)
    # ===================================================================== #
    # === seq4
    # ===================================================================== #
    when /seq4/
      @internal_hash[:array_sequences[3]] = only_valid_dna_nucleotides(a?)
    # ===================================================================== #
    # === agarose_table
    # ===================================================================== #
    when /agarose_?table/,
         /show_?agarose_?table/,
         /show_?agarose_?concentration/,
         'agarose'
      show_agarose_table
    # ===================================================================== #
    # === gene_name
    # ===================================================================== #
    when /gene_?name/,
         /set_?name_?of_?gene/,
         'gename',
         'set_name',
         'setname',
         'genename?',
         'setgene',
         'setgen',
         /name_?of_?gene/
      set_name_of_gene(a?)
    # ===================================================================== #
    # === codon_headers
    # ===================================================================== #
    when /codon(_|-)?headers/i,
         'codon_tables_headers',
         'codontablesheaders',
         'headercodon',
         'ctables',
         /^show(_|-)?all(_|-)?codon(_|-)?tables$/i
      show_all_codon_tables(:headers)
    # ===================================================================== #
    # === save?
    # ===================================================================== #
    when 'save?',
         /show_?save_?file/
      show_save_file
    # ===================================================================== #
    # === human_genome_version?
    #
    # Simply show the current human genome version.
    # ===================================================================== #
    when /human(_|-)?genome(_|-)?version\??/,
         /show(_|-)?human(_|-)?genome(_|-)?version$/i
      show_human_genome_version
    # ===================================================================== #
    # === show_aminoacids_residues
    # ===================================================================== #
    when /^show(_|-)?aminoacids(_|-)?residues$/i
      show_aminoacids_residues
    # ===================================================================== #
    # === save_here
    # ===================================================================== #
    when 'save_here',
         'savehere',
         /report(_|-| )?where(_|-| )?we(_|-| )?store$/i
      set_save_file(:default)
      report_where_we_store
    # ===================================================================== #
    # === show_codon_usage
    #
    # This entry point allows the user to analyse the codon usage of
    # the given argument.
    # ===================================================================== #
    when /codon(_|-| )?usage$/i,
         /show(_|-| )?codon(_|-| )?usage$/i,
         'cusage',
         'codo',
         'susage',
         /^-?-?codonusage\??$/i
      show_codon_usage(all_arguments?)
    # ===================================================================== #
    # === quit
    #
    # This entry point will honour all valid ways to exit,
    # store in the constant VALID_WAYS_TO_EXIT.
    # ===================================================================== #
    when *VALID_WAYS_TO_EXIT # bl $BIOROEBE/constants/constants.rb
      do_quit # Quit tag.
    else # else tag
      i = i.first if i.is_a? Array
      return if i.nil?
      # =================================================================== #
      # === First check whether we have a global environment variable.
      #
      # If so then this will be converted.
      # =================================================================== #
      i = convert_global_env(i) if i.to_s.include? '$'
      # =================================================================== #
      # === Handle ExpandCdAliases next
      #
      # Next, check whether we can use the cd-aliases.
      # =================================================================== #
      if use_expand_cd_aliases? and is_this_a_cd_alias?(i)
        target = ::Rcfiles::DirectoryAliases[i]
        cd(target)
      # =================================================================== #
      # === Handle existing local .pdb files next
      #
      # Since as of July 2022 this will also consider downloading
      # a remote .pdb file, if no such file exists yet - not in
      # this clause, but in the very next clause.
      # =================================================================== #
      elsif i and i.end_with?('.pdb') and File.exist?(i)
        parse_pdb_file(i)
      # =================================================================== #
      # === Download missing .pdb files here
      #
      # This must be closely kept in sync with the entry clause above.
      #
      # Usage example:
      #
      #   1hzh.pdb
      #
      # =================================================================== #
      elsif i.end_with?('.pdb') and !File.exist?(i.downcase)
        i = i.downcase
        unless File.exist?(::Bioroebe.pdb_directory?+File.basename(i))
          _result = download_this_pdb_file(i)
        else
          e 'The file already exists at `'+
             sfile(::Bioroebe.pdb_directory?+File.basename(i))+'`.'
        end
      # =================================================================== #
      # === Handle sequence assignments
      #
      # This entry clause is entered if the input consists of only valid
      # DNA nucleotides. Since as of December 2021 we will ignore
      # newlines that are part of the input sequence.
      #
      # Example to enter this clause:
      #
      #   ATGAGCAAGGCCGACTACGAGAAG
      #
      # =================================================================== #
      elsif only_valid_dna_nucleotides?(i.delete('-'))
        set_dna_sequence(i.delete('-'), :be_verbose) { :show_the_sequence_as_well }
      # =================================================================== #
      # === Handle downcased sequence assignments as well
      # =================================================================== #
      elsif only_valid_dna_nucleotides?(i.upcase.delete('-'))
        set_dna_sequence(i.upcase.delete('-'), :be_verbose)
      # =================================================================== #
      # === Handle input such as "227 / 3"
      # =================================================================== #
      elsif i.include?('/') and (i =~ /\d+/)
        result = eval(i)
        e result
      # =================================================================== #
      # === Intercept 3' input given to us.
      # =================================================================== #
      elsif original_input.to_s.strip.start_with?("3'-") # 3'-ATGCCTGCC
        find_complementary_strand(original_input)
      # =================================================================== #
      # === Handle WWW entries by opening them in the browser     (www tag)
      #
      # This includes "https" evidently as well.
      # =================================================================== #
      elsif i.start_with?('http')
        open_in_browser(i)
      # =================================================================== #
      # === Check for Aminoacids
      #
      # Check whether the input could be an Aminoacid such as Glycine.
      # =================================================================== #
      elsif could_this_be_an_amino_acid?(i)
        report_everything_about_this_amino_acid(i)
      # =================================================================== #
      # === Check for numbers as input only
      # =================================================================== #
      elsif (i =~ /^\d+$/) and (not main_sequence?.empty?)
        # ================================================================= #
        # Ok, the user did input only numbers. Display these numbers,
        # assumed to refer to the main sequence.
        # ================================================================= #
        _ = main_sequence?
        end_point = i.to_s.to_i - 1
        _ = _[0, end_point] # Must deduct one because we start nucleotide counting at nucleotide 1.
        erev properly_padded_dna_string(_)
      # =================================================================== #
      # === Handle remote fasta files and so forth
      # =================================================================== #
      elsif i.start_with?('http') and
          ( i.end_with?('.fasta') or i.end_with?('.fa') )
        erev 'We have encountered a remote file (fasta). We '\
             'will download it now.'
        this_file = download(i) # Also return this file.
        parse_fasta_format(this_file)
      # =================================================================== #
      # === Handle input starting with @
      # =================================================================== #
      elsif i.start_with? '@'
        e self.instance_variable_get(i)
      # =================================================================== #
      # === Handle nucleotide sequences next
      # =================================================================== #
      elsif is_all_upcase?(i) and only_valid_nucleotides?(i) and !i.empty?
        assign_dna_sequence(i, :be_verbose)
      # =================================================================== #
      # === Handle NCBI links next
      # =================================================================== #
      elsif i.start_with?('http://www.ncbi.') or
            i.start_with?('https://www.ncbi.')
        erev 'Identified a NCBI link. Will assume that this is a '\
             'fasta sequence'
        erev 'and delegate into the method called download_fasta().'
        download_fasta(i)
      # =================================================================== #
      # === Handle fasta input here if the file exists locally (files)
      #
      # This subsection will test for input that is about locally
      # existing files.
      # =================================================================== #
      elsif File.exist?(i) and !File.directory?(i)
        extname = File.extname(i).delete('.')
        case extname
        # ================================================================= #
        # === ps
        # ================================================================= #
        when 'ps' # check for .ps file type
          esystem "gv #{i}"
        # ================================================================= #
        # === fasta
        # ================================================================= #
        when 'fasta','fa'
          parse_fasta_format(i)
        else
          string_to_run = i.to_s+' '+f.to_s
          esystem(string_to_run)
        end
      # =================================================================== #
      # === Handle restriction enzymes
      # =================================================================== #
      elsif i.end_with?('?') or i.include?('Restriction') # if last character is a '?' character.
        @internal_hash[:result] = try_to_find_this_restriction_enzyme(i)
      # =================================================================== #
      # === Handle codons
      # =================================================================== #
      elsif (i.size == 3) and is_this_a_valid_codon?(i)
        e Bioroebe.dna_to_aminoacid_sequence(i)
      # =================================================================== #
      # === Next handle matches against the full line
      #
      # The input is: cytochrome c
      #
      # =================================================================== #
      elsif (original_input =~ /^-?-?cytochrome(_|-| )?c$/i)
        path = download(:cytochrome_c_protein_sequence)
        if File.exist? path
          parse_this_fasta_sequence(path)
        end
      else
        # ================================================================= #
        # === Check whether a local file exists like that
        #
        # The following code will check whether a file exists with the
        # same name in the log-directory. If so then it will be assigned
        # as input-name. Since this may be problematic, we put it into
        # the "else" clause.
        # ================================================================= #
        unless File.exist? i
          if File.exist?(::Bioroebe.log_dir?+i) and 
             File.file?(::Bioroebe.log_dir?+i) # ← Ensure that it really is a file.
            handle_this_file(::Bioroebe.log_dir?+i)
          end
        end
        # =================================================================== #
        # === Handle the case when we did not find the command
        #
        # This here is the final step - if we could not find anything
        # to do with the given input, we will report this to the user.
        # After all, perhaps he made a typo.
        # =================================================================== #
        if report_if_we_did_not_find_the_command # ← FINAL CHECK HERE
          # ================================================================= #
          # Handle .fasta or .fa files in a special way.
          # ================================================================= #
          unless i.empty?
            if i.end_with?('.fasta','fa') and !File.exist?(i)
              # ============================================================= #
              # In this case, try to also find a file with that name in the
              # log-directory of BioRoebe. That way, a user can just
              # copy/paste any URL or local path, and BioRoebe will try to
              # find a file that matches to this input.
              # ============================================================= #
              possible_location = log_dir?+File.basename(i)
              if File.exist? possible_location
                erev 'The given input was not found. However had, the '\
                     'same file was found at:'
                e "  #{sfancy(possible_location)}"
                erev 'This file will be used next.'
                handle_this_fasta_file(possible_location)
                return
              end
            end
            report_this_input_was_not_found(original_input)
          end
        end
      end
    end
  end
end

#runmode_is_commandline? ⇒ Boolean

#

runmode_is_commandline?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 10130

def runmode_is_commandline?
  runmode? == :commandline
end

#salt_adjusted_tm(i) ⇒ Object

#

salt_adjusted_tm

#


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# File 'lib/bioroebe/shell/shell.rb', line 6153

def salt_adjusted_tm(i)
  if i.is_a? Array
    i = i.join.strip
  end
  return ::Bioroebe.salt_adjusted_tm(i)
end

#sanitize_input(i) ⇒ Object

#

sanitize_input

Right now this method only gets rid of ‘-’ but check if the string contains ‘-’ first before calling this method.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8302

def sanitize_input(i)
  i.tr('-','')
end

#sanitize_nucleotide_sequence(i) ⇒ Object

#

sanitize_nucleotide_sequence

Invocation example:

sanitize_nucleotide_sequence "  10 AGTA \n  20 TTGC"
#


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# File 'lib/bioroebe/shell/shell.rb', line 11204

def sanitize_nucleotide_sequence(i)
  if i.is_a? Array
    i = i.join
  end
  @result = ::Bioroebe::SanitizeNucleotideSequence.new(i).result?.delete('"')
  set_dna_sequence(@result)
end

#save_file? ⇒ Boolean

#

save_file?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 5702

def save_file?
  @internal_hash[:save_file]
end

#save_history_to_file(dataset = ) ⇒ Object

#

save_history_to_file

This method will save the history to a local file.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8166

def save_history_to_file(
    dataset = array_history?[0..-2]
  )
  what = YAML.dump(dataset) # Save all but the last entry. Last entry will be "replay" usually.
  into = "#{log_dir?}replay_file.yml"
  write_what_into(what, into)
end

#save_my_file(&block) ⇒ Object

#

save_my_file (save tag)

We .strip on the @sequence because I think it is better to not have any padding on it.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2999

def save_my_file(&block)
  _ = dna_sequence_as_string?
  if _.empty?
    erev 'Can not save anything as the main string is empty.'
  else
    erev 'Saving the main string now into the file `'+
          sfile(save_file?)+
          rev+'`.'
    save_file(_.strip, save_file?)
  end # string must be empty.
end

#say_goodbye ⇒ Object

#

say_goodbye

#


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# File 'lib/bioroebe/shell/shell.rb', line 3275

def say_goodbye
  _ = ' '+version?.to_s
  _ = '' if _.size == 1
  erev "Bye from the BioShell#{_}!"
end

#scan_for_gff_files ⇒ Object

#

scan_for_gff_files

#


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# File 'lib/bioroebe/shell/shell.rb', line 5614

def scan_for_gff_files
  results_for_gff_files  = Dir['*.gff']
  results_for_gff3_files = Dir['*.gff3']
  unless results_for_gff_files.empty?
    erev 'There are '+sfancy(results_for_gff_files.size.to_s)+rev+
         ' .gff files in the current directory.'
  end
  unless results_for_gff3_files.empty?
    erev 'There are '+sfancy(results_for_gff3_files.size.to_s)+
         ' .gff3 files in the current directory.'
    erev 'We will simply pass the first entry there into '\
         'class Bioroebe::Parser::GFF.'
    parse_this_gff_file(results_for_gff3_files.first)
  end
end

#scan_for_leucine_zippers(i = amino_acid_sequence? ) ⇒ Object

#

scan_for_leucine_zippers

What is a leucine zipper?

https://en.wikipedia.org/wiki/Leucine_zipper
#


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# File 'lib/bioroebe/shell/shell.rb', line 9364

def scan_for_leucine_zippers(
    i = amino_acid_sequence?
  )
  if i.nil?
    i = amino_acid_sequence?
  end
  chars = i.chars
  # ======================================================================= #
  # We start to count at the first leucine zipper.
  # ======================================================================= #
  index = chars.index('L')
  erev 'The string '+simp(i)+rev+' has these at every 7th step.'
  print '  ' # Leading indent.
  (index..chars.size).step(7) {|token|
    print simp(chars[token]),' '
  }; e # And a final newline.
end

#scan_or_parse_for_this_gff_file_or_any_gff_file(i) ⇒ Object

#

scan_or_parse_for_this_gff_file_or_any_gff_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 5633

def scan_or_parse_for_this_gff_file_or_any_gff_file(i)
  if i.is_a? Array
    i.each {|entry|
      if entry.nil?
        scan_for_gff_files
      else
        scan_or_parse_for_this_gff_file_or_any_gff_file(entry)
      end
    }
  else
    if File.exist? i.to_s
      parse_this_gff_file(i)
    else # else scan for any .gff or .gff3 file.
      scan_for_gff_files
    end
  end
end

#search_for(i, be_verbose = true) ⇒ Object

#

search_for (search_for tag)

This method essentially combines the two methods set_search_for() and start_search().

#


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# File 'lib/bioroebe/shell/shell.rb', line 3166

def search_for(
    i, be_verbose = true
  )
  if i.is_a? Array
    i = i.join(' ').strip
  end
  set_search_for(i, be_verbose)
  start_search(be_verbose)
end

#search_for? ⇒ Boolean

#

search_for?

This method can be queried from the interactive-bioshell via:

search_for?
#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7395

def search_for?
  @internal_hash[:search_for]
end

#search_for_known_promoters ⇒ Object

#

search_for_known_promoters

This method will attempt to identify promoter elements.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3148

def search_for_known_promoters
  erev 'Next searching for known promoters.'
  e
  erev "35S Promoter (#{sfancy('TGAGACTTTT')}#{rev}):"
  how_many_35S_promoters_are_in_the_sequence = 
    search_for 'TGAGACTTTT', :be_quiet
  if how_many_35S_promoters_are_in_the_sequence > 0
    erev 'There appears to be at the least one 35S promoter '\
         'in the target sequence.' 
  end
end

#search_for_nucleotide_sequence(i) ⇒ Object

#

search_for_nucleotide_sequence

This method will use the NCBI interface to search for nucleotide sequences.

Usage example:

snuc lady slipper orchid
#


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# File 'lib/bioroebe/shell/shell.rb', line 7984

def search_for_nucleotide_sequence(i)
  i = i.join '+' if i.is_a? Array
  open_in_browser "https://www.ncbi.nlm.nih.gov/nucgss?term=#{i}"
end

#search_for_tata_consensus_sequence ⇒ Object

#

search_for_tata_consensus_sequence

Use this method to search for a TATA consensus sequence in the target string (the so-called “TATA box”). The TATA box is an AT-rich sequence that can be found upstream of the transcription start site.

A short overview of this sequence format can be found here:

https://en.wikiversity.org/wiki/Gene_transcriptions/Boxes/TATA#Consensus_sequence

The major consensus sequence is:

3'-TATAAA-5'

This is just the major one; there are variants of this sequences such as

3'-TATAAA(A)AAA-5'

And similar variants.

Usage example:

set_string GGGCTATAAAAATTGGGATATAAAATTGTATATA; find_TATA?
#


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# File 'lib/bioroebe/shell/shell.rb', line 10061

def search_for_tata_consensus_sequence
  full_sequence = sequence? # Grab hold of the sequence.
  # ======================================================================= #
  # Next define our TATA box which we will try to discover:
  # ======================================================================= #
  tata_box_sequence = 'TATAAA'
  results = full_sequence.scan(/#{tata_box_sequence}/)
  if results.empty?
    erev 'Our target string (length: '+full_sequenze.size.to_s+') '\
         'does not include `'+
         simp(tata_box_sequence)+rev+'`.'
  else
    n_results = results.size.to_s # <- Determine how many matches were found.
    erev "We did find #{simp(n_results)} "\
         "#{sfancy(tata_box_sequence)}#{rev} entries."
    erev 'Their starting positions are at:'
    array = []
    splitted_sequence = full_sequence.split(//)
    splitted_sequence.each_with_index {|entry, index|
      case entry
      when 'T' # This could be a TATA sequence.
        # ================================================================= #
        # Next we will compare whether the sequence matches.
        # ================================================================= #
        subsequence = full_sequence[index, tata_box_sequence.size]
        if tata_box_sequence == subsequence
          array << index # <- Append into our Array here.
        end
      end
    }
    e
    print '  '
    pp array
    # ===================================================================== #
    # As of May 2016 we will also use find() to find the TATA box.
    # ===================================================================== #
    e
    erev 'We will also show the sequence in a highlighted manner next:'
    e
    try_to_find_restriction_enzymes_for(tata_box_sequence)
  end
end

#search_sequence_for_open_reading_frames(i = :default, use_which_frame = :frame1, use_this_start_codon = :default) ⇒ Object

#

search_sequence_for_open_reading_frames

Use this method to search for Open Reading Frames (i.e. “AUG” codons).

Since we use Bioroebe.start_codon?, this may also default to another start codon.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5457

def search_sequence_for_open_reading_frames(
    i                    = :default,
    use_which_frame      = :frame1,
    use_this_start_codon = :default
  )
  case use_this_start_codon
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    use_this_start_codon = ::Bioroebe.start_codon?
  end
  case i
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    i = string?
  end
  i.upcase!
  if i
    if i.include? use_this_start_codon # This asks whether the string includes 'ATG'.
      report_n_start_codons # Will report how many Start sequences we have.
      e
      erev "These can be found (and will start) at these positions"
      erev "(later shown via red colour):#{N}#{N}"
      copy = i.to_s.dup # Work on a copy here.
      if use_which_frame == :frame2 # Chop off the first entry then.
        copy[0,1] = ''
      end
      # =================================================================== #
      # We will search for both ATG and AUG though, respectively the
      # input variants given to us. If the following regex appears to
      # be complicated to you, here is the old variant for the regex:
      #
      #   use_this_regex = /(ATG|AUG)/i
      #
      # =================================================================== #
      array_results = []
      array_results << Bioroebe.return_array_of_sequence_matches(copy, use_this_start_codon)
      if use_this_start_codon.include? 'T'
        array_results << Bioroebe.return_array_of_sequence_matches(copy, use_this_start_codon.tr('T','U'))
      end
      array_results.flatten!
      array_results.compact!
      # =================================================================== #
      # This will hold data such as:
      #   [16, ["ATG"]]
      # At the least up until April 2020, before it was changed.
      # =================================================================== #
      return array_results
    else
      []
    end
  else
    ewarn 'It seems as if you have not yet assigned a string.'
    ewarn 'You could run "random" to assign a random string.'
  end
end

#second_argument? ⇒ Boolean Also known as: second_argument

#

second_argument?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7454

def second_argument?
  @internal_hash[:all_arguments][1]
end

#sequence_2 ⇒ Object Also known as: seq2, seq2?

#

sequence2

#


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# File 'lib/bioroebe/shell/shell.rb', line 7019

def sequence_2
  @sequence_2.to_str
end

#sequence_3 ⇒ Object Also known as: seq3, seq3?

#

sequence3

#


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# File 'lib/bioroebe/shell/shell.rb', line 6987

def sequence_3
  @sequence_3.to_str
end

#sequence_4 ⇒ Object Also known as: seq4, seq4?

#

sequence4

#


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# File 'lib/bioroebe/shell/shell.rb', line 6995

def sequence_4
  @sequence_4.to_str
end

#sequence_5 ⇒ Object Also known as: seq5, seq5?

#

sequence5

#


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# File 'lib/bioroebe/shell/shell.rb', line 7003

def sequence_5
  @sequence_5.to_str
end

#sequence_6 ⇒ Object Also known as: seq6, seq6?

#

sequence6

#


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# File 'lib/bioroebe/shell/shell.rb', line 7011

def sequence_6
  @sequence_6.to_str
end

#set_aminoacids(i = :random, how_many_to_generate = :default, be_verbose = true) ⇒ Object Also known as: assign_aminoacid_sequence, assign_protein_sequence, set_aminoacid_sequence

#

set_aminoacids (assign protein tag, set aminoacids tag)

Assign a protein sequence here. The first argument shall be the aminoacid sequence in question.

Usage example:

assign_protein FLIMVSPTAYHQNKDECWRGX*
#


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# File 'lib/bioroebe/shell/shell.rb', line 1075

def set_aminoacids(
    i                    = :random,
    how_many_to_generate = :default, # Will only be applied if the input is :random or :generate
    be_verbose           = true
  )
  case how_many_to_generate
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    how_many_to_generate = 1000
  end
  # ======================================================================= #
  # === Sanitize the third argument next
  # ======================================================================= #
  case be_verbose
  when :be_silent,
       :be_quiet
    be_verbose = false
  end
  i = :random unless i
  case i
  # ======================================================================= #
  # === :random
  # ======================================================================= #
  when :random,
       :generate 
    i = Bioroebe.create_random_aminoacids(how_many_to_generate) # Generate them here.
  end
  i = i.join if i.is_a? Array
  if i.is_a?(String) and i =~ /^\d+$/ # only numbers
    i = Bioroebe.create_random_aminoacids(i)
  end
  if i.is_a? String # Convert it into a Sequence object here.
    i = ::Bioroebe.sequence(i) { :aminoacid }
  end
  i = i.dup
  if i.is_a?(Bioroebe::ConvertThisCodonToThatAminoacid)
    i = i.sequence?
  end
  i.upcase!
  if be_verbose
    erev "Now assigning aminoacid sequence to: #{sfancy(i.to_s)}"
  end
  # ======================================================================= #
  # Do the assignment next.
  # ======================================================================= #
  if @internal_hash[:array_aminoacid_sequence].empty?
    @internal_hash[:array_aminoacid_sequence] << i
  else
    @internal_hash[:array_aminoacid_sequence].pop
    @internal_hash[:array_aminoacid_sequence] << i
  end 
end

#set_codon_table(i) ⇒ Object

#

set_codon_table

Set which codon table to use.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3090

def set_codon_table(i)
  ::Bioroebe.set_codon_table(i, :be_verbose) # defined in codon_table.rb
end

#set_default_highlight_colour ⇒ Object

#

set_default_highlight_colour

#


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# File 'lib/bioroebe/shell/shell.rb', line 8670

def set_default_highlight_colour
  @highlight_colour = Colours::YELLOW # So to avoid a warning if we were to use the method.
end

#set_default_length(i = DEFAULT_LENGTH_FOR_DNA, be_verbose = false) ⇒ Object Also known as: set_maxlength

#

set_default_length

#


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# File 'lib/bioroebe/shell/shell.rb', line 7128

def set_default_length(
    i          = DEFAULT_LENGTH_FOR_DNA,
    be_verbose = false
  )
  case be_verbose
  when :be_verbose
    be_verbose = true
  end
  if i.is_a? Array
    i = i.join(' ').strip
  end
  i = i.to_i
  if be_verbose
    erev 'Setting to a default length of `'+simp(i.to_s)+rev+'` next.'
  end
  @internal_hash[:default_length] = i
end

#set_download_directory(i = ::Bioroebe.log_dir?) ⇒ Object

#

set_download_directory

#


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# File 'lib/bioroebe/shell/shell.rb', line 10270

def set_download_directory(
    i = ::Bioroebe.log_dir?
  )
  i = i.to_s
  erev "Setting the download directory to #{simp(i)}#{rev} next:"
  ::Bioroebe.set_log_dir(i)
end

#set_exit_gracefully ⇒ Object

#

set_exit_gracefully

#


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# File 'lib/bioroebe/shell/shell.rb', line 9960

def set_exit_gracefully
  @internal_hash[:exit_the_shell_how] = :exit_gracefully
end

#set_highlight_colour(i = :violet, be_verbose = false) ⇒ Object

#

set_highlight_colour

You can use this method to highlight different substrings.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9588

def set_highlight_colour(
    i          = :violet,
    be_verbose = false
  )
  if be_verbose == :be_verbose
    be_verbose = true
  end
  i = i.to_s unless i.is_a? String
  case i
  when 'random'
    i = ::Colours.random_html_colour
  end
  if i
    if be_verbose
      erev "We will use the colour #{sfancy(i.to_s)}#{rev}"\
           " for highlighting important subsequences."
    end
    if ::Colours.respond_to? i
      i = ::Colours.send(i) # Assume that the user wants to use a KDE Konsole colour.
    else # else Konsole does not respond to this particular colour.
      erev "You are trying to use the colour #{i}"
      erev 'This is not part of the Colours namespace, though. '\
           'If you are trying to use a'
      erev 'colour, you may want to pick another colour.'
    end
  end
  @highlight_colour = i
end

#set_highlight_colour_or_search_for_this_sequence(i, be_verbose = false) ⇒ Object

#

set_highlight_colour_or_search_for_this_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 9520

def set_highlight_colour_or_search_for_this_sequence(
    i, be_verbose = false
  )
  # ======================================================================= #
  # First check if the input consists of only upcased characters.
  # ======================================================================= #
  if (i == i.upcase)
    report_main_sequence(i)
  else
    set_highlight_colour(i, be_verbose)
  end
end

#set_jumper_directory(i) ⇒ Object

#

set_jumper_directory

#


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# File 'lib/bioroebe/shell/shell.rb', line 9791

def set_jumper_directory(i)
  if i
    erev 'Adding '+sdir(i)+' to the jumper directories.'
    @internal_hash[:array_jumper_directories] << i
  end
end

#set_locus(i) ⇒ Object

#

set_locus

#


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# File 'lib/bioroebe/shell/shell.rb', line 7567

def set_locus(i)
  @internal_hash[:locus] = i
end

#set_log_dir(i = first_argument? ) ⇒ Object

#

set_log_dir

#


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# File 'lib/bioroebe/shell/shell.rb', line 2575

def set_log_dir(
    i = first_argument?
  )
  i = i.dup if i.frozen?
  i << '/' unless i.end_with? '/'
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    when :be_verbose
      erev 'Will be using '+sdir(i)+rev+' as the new log-directory.'
    end
  end
  unless File.directory? i
    mkdir(i)
  end
  ::Bioroebe.set_log_dir(i)
end

#set_mode(i = :dna) ⇒ Object

#

set_mode

#


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# File 'lib/bioroebe/shell/shell.rb', line 10849

def set_mode(i = :dna)
  case i
  when :protein, :proteins # Aliases.
    i = :aminoacids
  end
  @internal_hash[:mode] = i
end

#set_name_of_gene(i = '', be_verbose = :be_verbose) ⇒ Object

#

set_name_of_gene

Use this method to set the name of a gene in question.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6420

def set_name_of_gene(
    i          = '',
    be_verbose = :be_verbose
  )
  case be_verbose
  when :be_verbose
    be_verbose = true
  end
  if i.is_a? Array # We don't want Arrays here.
    i = i.join(' ').strip
  end
  if i.nil? or i.to_s.empty?
    erev 'Please assign a non-empty name for the gene.'
    return
  end
  if be_verbose
    erev 'Now assigning the gene name to "'+simp(i)+rev+'", without '\
         'the quotes.'
  end
  sequence_object?.name_of_gene = i
end

#set_nucleotide_sequence(i = nil, be_verbose = false, do_upcase = :check_for_config_value_here, &block) ⇒ Object Also known as: set_dna_sequence, set_DNA_sequence, assign_sequence, set_sequence, assign_dna_sequence, assign_this_dna_sequence, assign, set_dna_string, set_string, set_main_sequence, set_dna, set_assign, set_raw_sequence

#

set_nucleotide_sequence (assign tag, assigning tag)

This method can be used to set/assign to the main DNA string in use, also called the “main nucleotide sequence”.

This method is fairly long, mostly because it will do lots of additional tasks, way aside from setting/assigning to a DNA sequence only. This makes it a bit difficult to change, so ideally we should avoid adding code that is not really necessary here.

Since as of June 2016, the method will also keep a backup of the generated sequence in a local file as well. This will allow us to “replay” the given sequence on startup of the shell.

Note that as of Jun 2016, we will chop off any ‘“’ found in the input String.

#


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# File 'lib/bioroebe/shell/shell.rb', line 11231

def set_nucleotide_sequence(
    i          = nil,
    be_verbose = false,
    do_upcase  = :check_for_config_value_here,
    &block
  )
  # ======================================================================= #
  # First check whether the main sequence is frozen:
  # ======================================================================= #
  if is_the_main_sequence_frozen?
    report_that_the_main_sequence_is_frozen
    return
  end
  case do_upcase
  # ======================================================================= #
  # === :check_for_config_value_here
  # ======================================================================= #
  when :check_for_config_value_here,
       :default
    if @configuration and @configuration.respond_to?(:upcase_nucleotides)
      do_upcase = @configuration.upcase_nucleotides
    else
      do_upcase = false
    end
  # ======================================================================= #
  # === :do_not_upcase
  # ======================================================================= #
  when :do_not_upcase
    do_upcase = false
  end
  # ======================================================================= #
  # === Sanitize the second variable next
  # ======================================================================= #
  case be_verbose
  # ======================================================================= #
  # === :be_verbose
  # ======================================================================= #
  when :be_verbose
    be_verbose = true
  # ======================================================================= #
  # === :do_not_upcase
  # ======================================================================= #
  when :do_not_upcase,
       :no_upcase,
       :no_upcasing,
    shall_we_upcase = false
    be_verbose = true # Sync this.
  # ======================================================================= #
  # === :be_silent
  # ======================================================================= #
  when :be_silent,
       :be_quiet
    be_verbose = false
  end
  # ======================================================================= #
  # === Convert Array into String next
  # ======================================================================= #
  i = i.join if i.is_a? Array
  # ======================================================================= #
  # === Handle Fasta format next (the input may be an Integer, so we have
  #     to use .to_s here)
  # ======================================================================= #
  if i and i.to_s.start_with?('>') and i.to_s.include?(N)
    erev 'It seems as if you have a FASTA sequence there, as it '\
         'starts with a > character.'
    erev 'We will omit this first section (the header) though.'
    i[0 .. i.index(N)] = '' # This does the chop-off action.
  end
  if i.nil?
    # ===================================================================== #
    # === Hande nil value for the variable i next:
    #
    # In this entry point, we will handle if the first input argument
    # is nil.
    #
    # If @internal_hash[:misc_sequence] is NOT nil, then it will be used
    # once, then cleared. Otherwise, we will use dna_sequence?.
    # ===================================================================== #
    if @internal_hash[:misc_sequence]
      i = @internal_hash[:misc_sequence]
      @internal_hash[:misc_sequence] = nil # Set it to nil again.
    else
      i = dna_sequence?
    end
  end
  if i and i.to_s.include? ' ' # Sanitize the input a little bit.
    i = i.strip.delete(' ')
  end
  if i.to_s.include? '|' # I think we will not need '|' in our main string.
    i.delete!('|')
  end
  # ======================================================================= #
  # === If the input has only numbers
  # ======================================================================= #
  if i.is_a?(Numeric) or (i =~ /^\d+$/)
    i = random_dna_sequence(i)
  end
  i = i.to_s # Work on a String past this point here.
  # ======================================================================= #
  # Assume a file was given. Read its content then.
  # ======================================================================= #
  if File.exist?(i)
    if i.end_with? '.yml'
      i = YAML.load_file(i)
    else
      i = File.readlines(i).reject {|line|
        line.start_with? '>'
      }.join
    end
  end
  # ======================================================================= #
  # Unfreeze Strings if necessary:
  # ======================================================================= #
  i = i.dup if i.frozen?
  if i.nil? or i.empty?
    erev 'Missing Input to set_nucleotide_sequence(). Please input '\
         'your DNA string now (Hitting the enter key will finish this):'
    i = $stdin.gets.chomp
    i = i.upcase if shall_we_upcase
  end
  # ======================================================================= #
  # === Handle special sequences (nucleotide sequences) next
  # ======================================================================= #
  case i
  # ======================================================================= #
  # === :GFP
  #
  # Usage example:
  #
  #   setsequence :GFP
  #
  # ======================================================================= #
  when ':GFP' # ← This means the default GFP sequence.
    i = return_default_GFP_sequence
  # ======================================================================= #
  # === random
  #
  # Usage example:
  #
  #   setsequence random
  #
  # ======================================================================= #
  when /^random$/i,
       '' # As of 04.01.2015, we will try '' too here.
    i = return_a_random_sequence_of_n_nucleotides
  # ======================================================================= #
  # === multiline
  # ======================================================================= #
  when 'multiline' # Handle multiline input.
    erev 'Multiline input detected.'
    erev 'Finish by issuing __ on an empty line. (These are 2 "_" tokens.)'
    i = $stdin.gets('__')
    # ===================================================================== #
    # Next, sanitize it a bit if it starts with a '>' identifier.
    # ===================================================================== #
    if i.strip.start_with? '>'
      i = i[(i.index(N)+1)..-1]
    end
  end
  # ======================================================================= #
  # Also get rid of numbers.
  # ======================================================================= #
  i.gsub!(/\d/,'')
  i.delete!('-') if i.include? '-'
  i.delete!('_') if i.include? '_' # Don't want '_' characters.
  i.delete!('?') if i.include? '?'
  i.delete!('#') if i.include? '#' # This was added at 08.05.2016.
  i.delete!('"') if i.include? '"' # This was added at 02.06.2016.
  # ======================================================================= #
  # === Remove possible newlines in the given input
  # ======================================================================= #
  i.delete!(N)   if i.include? N
  # i.delete!('_') if i.include? '_'
  i.gsub!(/\^C/,'') if i.include? '^C'
  # ======================================================================= #
  # === Next upcase the input if the flag was set
  # ======================================================================= #
  if do_upcase
    i.upcase!
  end
  # ======================================================================= #
  # === Check for verbosity next:
  # ======================================================================= #
  if be_verbose
    msg = 'Assigning a '.dup
    if mode? == :dna
      msg << 'DNA '
    end
    msg << "sequence next, containing "\
           "#{steelblue(i.size.to_s)}#{rev} nucleotides."
    # ===================================================================== #
    # === Report that we will perform an assignment next in this case
    #  ==================================================================== #
    erev msg
  end
  # ======================================================================= #
  # === :coding_area
  #
  # Whenever the DNA sequence is modified like that, we will also reset
  # the "coding_area" entry in the internal Hash to the initial nil state.
  # ======================================================================= #
  @internal_hash[:coding_area] = nil if i and !i.empty?
  # ======================================================================= #
  # Finally assign it to the last nucleotide sequence:
  # ======================================================================= #
  last_nucleotide_sequence?.set_sequence(i)
  # ======================================================================= #
  # Next we will save into a file, but not empty nucleotide Strings,
  # hence the check:
  # ======================================================================= #
  unless i.empty?
    # ===================================================================== #
    # We will save into a file next.
    # ===================================================================== #
    this_file = "#{log_dir?}bioshell/dna_string.yml"
    last_nucleotide_sequence?.save_sequence_to_this_file(this_file) # Save it here.
  end
  # ======================================================================= #
  # === "Automatically" update the aminoacid sequence as well
  #     afterwards:
  # ======================================================================= #
  aminoacid_sequence = translate_dna_into_aminoacid(i)
  set_aminoacids(aminoacid_sequence, :default, :be_quiet) # Second argument is n aminoacids to generate.
  # ======================================================================= #
  # Since as of Jun 2016, we will also create a new RNA string.
  #
  # This has been disabled as of December 2021. It was too strange
  # to automatically create a RNA string. One may question whether
  # the aminoacid sequence should be automatically created, but I
  # found this to be useful, so who knows - perhaps creating a
  # corresponding RNA sequence may be re-added one day in the
  # future.
  # ======================================================================= #
  # if @internal_hash[:array_rna_sequence]
  #   @internal_hash[:array_rna_sequence].last.set_sequence(result)
  # end
  # ======================================================================= #
  # === Set the Xorg Buffer next, if the configuration mandates this
  # ======================================================================= #
  if @configuration and @configuration.respond_to?(:additionally_set_xorg_buffer) and
     @configuration.additionally_set_xorg_buffer
    begin
      set_xorg_buffer(i)
    rescue NoMethodError; end
  end
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :show_the_sequence_as_well
    # ===================================================================== #
    when :show_the_sequence_as_well
      show_DNA_sequence
    end
  end
  return i # And return it, just in case.
end

#set_padding(i = DEFAULT_PADDING, be_verbose = :be_quiet) ⇒ Object

#

set_padding

This method allows us to set the default (left) padding that we may display for DNA strings.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4299

def set_padding(
    i          = DEFAULT_PADDING,
    be_verbose = :be_quiet
  )
  case be_verbose
  when :be_quiet
    be_verbose = false
  when :be_verbose
    be_verbose = true
  end
  case i.to_s
  when /(\d{1,3})/
    i = ' ' * $1.to_s.dup.to_i
  when 'default'
    i = DEFAULT_PADDING
  end
  if be_verbose
    erev 'The new padding will have '+sfancy(i.count(' ').to_s)+rev+
         ' space characters.'
  end
  @internal_hash[:padding] = i
end

#set_random_aminoacids ⇒ Object

#

set_random_aminoacids

Simply delegate to set_aminoacids.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7590

def set_random_aminoacids
  set_aminoacids :random
end

#set_result(i) ⇒ Object

#

set_result

#


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# File 'lib/bioroebe/shell/shell.rb', line 820

def set_result(i)
  @internal_hash[:result] = i
end

#set_save_file(i = :default) ⇒ Object

#

set_save_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 5675

def set_save_file(
    i = :default
  )
  case i
  # ======================================================================= #
  # === :default_fasta
  # ======================================================================= #
  when :default_fasta
    i = return_pwd+'standard_fasta.fa'
  # ======================================================================= #
  # === :pwd
  # ======================================================================= #
  when :pwd
    return_pwd+File.basename(save_file?)
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    i = Bioroebe.log_dir?+
        File.basename(save_file?)
  end
  @internal_hash[:save_file] = i
end

#set_search_for(i, be_verbose = true) ⇒ Object Also known as: set_search_string

#

set_search_for

This setter-method can be used to designate for which subsequence we may search-for, if this is necessary, e. g. to detect “AUG” in a sequence of “GGCAUGGGC”.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7996

def set_search_for(
    i, be_verbose = true
  )
  case be_verbose
  when :be_quiet
    be_verbose = false
  end
  i = i.join if i.is_a? Array
  if be_verbose
    erev "We will now search for: #{simp(i.to_s)}" if i
  end
  @internal_hash[:search_for] = i
end

#set_sequence_2(i = '') ⇒ Object

#

set_sequence_2

#


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# File 'lib/bioroebe/shell/shell.rb', line 8376

def set_sequence_2(i = '')
  i = i.join(' ').strip if i.is_a? Array
  i.delete!(N)
  i = i.to_str unless i.is_a? String
  @sequence_2 = ::Bioroebe.sequence(i)
end

#set_sequence_3(i = '') ⇒ Object

#

set_sequence_3

#


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# File 'lib/bioroebe/shell/shell.rb', line 8386

def set_sequence_3(i = '')
  i = i.join(' ').strip if i.is_a? Array
  i.delete!(N)
  i = i.to_str unless i.is_a? String
  @sequence_3 = ::Bioroebe.sequence(i)
end

#set_sequence_4(i = '') ⇒ Object

#

set_sequence_4

#


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# File 'lib/bioroebe/shell/shell.rb', line 8396

def set_sequence_4(i = '')
  i = i.join(' ').strip if i.is_a? Array
  i.delete!(N)
  i = i.to_str unless i.is_a? String
  @sequence_4 = ::Bioroebe.sequence(i)
end

#set_sequence_5(i = '') ⇒ Object

#

set_sequence_5

#


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# File 'lib/bioroebe/shell/shell.rb', line 8406

def set_sequence_5(i = '')
  i = i.join(' ').strip if i.is_a? Array
  i.delete!(N)
  i = i.to_str unless i.is_a? String
  @sequence_5 = ::Bioroebe.sequence(i)
end

#set_sequence_6(i = '') ⇒ Object

#

set_sequence_6

#


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# File 'lib/bioroebe/shell/shell.rb', line 5165

def set_sequence_6(i = '')
  i = i.join(' ').strip if i.is_a? Array
  i.delete!(N)
  i = i.to_str unless i.is_a? String
  @sequence_6 = ::Bioroebe.sequence(i)
end

#set_start_codon(i = nil) ⇒ Object

#

set_start_codon

If you wish to use another start codon, this is the right method.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9703

def set_start_codon(i = nil)
  i = i.to_s
  i.tr!('U','T')
  if i.empty?
    erev 'Please assign a non-empty start codon.'
  else
    erev 'Setting to use this as start codon next: '+
          simp(i)
    ::Bioroebe.set_start_codon(i)
  end
end

#set_use_this_prompt(i = NAME_OF_BIO_SHELL) ⇒ Object Also known as: set_prompt

#

set_use_this_prompt

This method can be used to set the prompt of the bio-shell.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9387

def set_use_this_prompt(i = NAME_OF_BIO_SHELL)
  case i # case tag
  # ======================================================================= #
  # === NONE
  # ======================================================================= #
  when /^NONE$/i,
       'empty',
       :empty
    i = "\n"
    do_not_use_working_directory_as_prompt
  # ======================================================================= #
  # === pwd
  # ======================================================================= #
  when 'pwd', :cwd, nil 
    i = return_default_prompt
    do_use_working_directory_as_prompt
  # ======================================================================= #
  # === REVERT
  # ======================================================================= #
  when /^REVERT$/i,
       /^DEFAULT$/i,
       :default
    i = NAME_OF_BIO_SHELL
    do_not_use_working_directory_as_prompt
  end
  @internal_hash[:prompt_to_use] = i
end

#set_user_input(i) ⇒ Object

#

set_user_input

#


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# File 'lib/bioroebe/shell/shell.rb', line 11750

def set_user_input(i)
  @internal_hash[:user_input] = i
end

#set_xclip(i = dna_string? ) ⇒ Object

#

set_xclip (xclip tag, xorg tag, buffer tag)

Use this method to assign to the Linux Xorg Buffer.

By default we will assign the DNA nucleotide sequence to be the new buffer.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5076

def set_xclip(
    i = dna_string?
  )
  XorgBuffer.set_xorg_buffer(i)
end

#setup_readline ⇒ Object

#

setup_readline

We will make use of the constant COMPLETION_PROC for the readline component.

#


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# File 'lib/bioroebe/shell/readline.rb', line 66

def setup_readline
  Readline.completion_append_character = ' '
  Readline.completion_proc = COMPLETION_PROC
end

#shorten_aminoacid(these_aminoacids = aminoacid_sequence? ) ⇒ Object

#

shorten_aminoacid

This method will translate an Aminoacid from Lys to K.

Usage example:

shorten Lys Val His His Leu Met Ala Ala Lys
#


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# File 'lib/bioroebe/shell/shell.rb', line 2153

def shorten_aminoacid(
    these_aminoacids = aminoacid_sequence?
  )
  unless these_aminoacids
    erev 'Please either assign an aminoacid sequence prior to invoking'
    erev 'this method or simply pass in the aminoacids that you wish'
    erev 'to short. Example:'
    erev '  shorten Lys Val His'
    return
  end
  erev N+'Now translating three letter Aminoacid to their one '\
       'letter representation: '+N+'  '+sfancy(these_aminoacids)+rev+N
  if these_aminoacids.include? ' '
    these_aminoacids.delete!(' ') # get rid of ' '
  end
  if these_aminoacids.include? '-'
    these_aminoacids = sanitize_input(these_aminoacids)
  end
  # ========================================================================= #
  # Instantiate a new Bioroebe object next.
  # ========================================================================= #
  @bioroebe = ::Bioroebe.new(these_aminoacids)
  erev '  '+@bioroebe.three_to_one+N
  _ = @bioroebe.three_to_one
  e
  erev 'Next we will show the available codons for these aminoacids:'
  e
  _.scan(/./).each { |f|
    erev '  '+f+' -> '+
         '['+@bioroebe.aminoacid_to_codon(f).join(', ')+']'
  }
  e
end

#show(i) ⇒ Object

#

show (show tag)

Bundle together some show-related methods.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1818

def show(i)
  i = i.join(' ').strip if i.is_a? Array
  case i
  when 'codon_table','codon','codon table'
    show_codon_table
  when 'blosum','blosum matrix','blosum_matrix'
    show_blosum_matrix
  when '',nil # Empty or nil.
    show_dna_string
  end
end

#show_2D_dotplot(string1 = nil, string2 = nil) ⇒ Object

#

show_2D_dotplot

#


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# File 'lib/bioroebe/shell/shell.rb', line 2315

def show_2D_dotplot(
    string1 = nil, string2 = nil
  )
  if string1.nil? and string2.nil?
    erev 'You want to use a dotplot.'
    erev 'Please provide the first string, which will be on the left side:'
    string1 = $stdin.gets.chomp
    erev 'Please provide the second string, which will be on the top side:'
    string2 = $stdin.gets.chomp
  end
  ::Bioroebe::AdvancedDotplot.new(string1, string2)
end

#show_agarose_table ⇒ Object

#

show_agarose_table

This method will simply show common agarose concentrations.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4713

def show_agarose_table
  hash = load_bioroebe_yaml_file(:agarose)
  e
  e 'Agarose concentrations:'
  e
  hash.each_pair {|concentration_of_the_gel, kb_fragment|
    erev '  A concentration of '+simp(concentration_of_the_gel.to_s+'%')+
         rev+' will separate DNA fragments between '+sfancy(kb_fragment)+
         rev+' kb.'
  }; e
end

#show_all_codon_tables(show_what = :everything) ⇒ Object

#

show_all_codon_tables

We used to tap into the Bio::CodonTable here for this part.

But since some time, we no longer depend on this part - we have made available all of this in yaml files.

The argument to this method can either be:

:everything
:only_names

The first one is the default. This means that we will show everything.

The second version is useful if you only what to report the names of the codon table in question. Several aliases exist for the second invocation.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6595

def show_all_codon_tables(
    show_what = :everything
  )
  unless Bioroebe.const_defined? :ShowCodonTables
    require 'bioroebe/codons/show_codon_tables.rb'
  end
  e
  ::Bioroebe::ShowCodonTables.new(show_what)
  e
end

#show_all_deducible_aminoacid_sequences(i = dna_sequence_as_string?, , also_show_numbers = true, show_translations_aligned = true) ⇒ Object

#

show_all_deducible_aminoacid_sequences

Note that if the string is too short, we won’t display the other frames.

If the third argument, ‘show_translations_aligned`, is set to true then we will additionally display all 3 frames aligned one to another.

Usage example:

toproteins AUG
toproteins AUGAUGUUGAAU
toproteins AUG-AUG-UUG-AAA-GGU-CGC-AAU-STOP
#


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# File 'lib/bioroebe/shell/shell.rb', line 5291

def show_all_deducible_aminoacid_sequences(
    i                         = dna_sequence_as_string?,
    also_show_numbers         = true,
    show_translations_aligned = true
  )
  if i and i.is_a?(Array) and i.empty?
    i = dna_sequence_as_string?
  end
  i = dna_sequence_as_string? if i.nil?
  i = i.join(' ').strip if i.is_a? Array
  i = i.to_s.dup # To avoid nil-operations.
  i.delete!('-') if i.include? '-'
  if i.empty? # This means that the user has not yet assigned a DNA sequence.
    erev 'Please assign some DNA sequence. You can also randomly generate'
    erev 'a new sequence via "random".'
    return
  end
  cliner
  erev N+'The amino acid sequence for '+sfancy('Frame 1')+rev+' is: '
  e
  converted_sequence_for_frame_1 = translate_dna_into_aminoacid(i).to_s
  erev '  '+converted_sequence_for_frame_1+N+N
  # ======================================================================= #
  # === Also show numbers
  # ======================================================================= #
  if also_show_numbers
    verbose_report_numbered_amino_acid_sequence(converted_sequence_for_frame_1)
  end
  cliner
  if i && i.size > 2
    erev N+N+'The amino acid sequence for '+sfancy('Frame 2')+rev+' is: '
    e
    converted_sequence_for_frame_2 = translate_dna_into_aminoacid_frame2(i)
    erev '  '+converted_sequence_for_frame_2+N+N
    if also_show_numbers
      verbose_report_numbered_amino_acid_sequence(converted_sequence_for_frame_2, '2')
    end
    cliner
    e
    erev N+N+'The amino acid sequence for '+sfancy('Frame 3')+rev+' is: '
    e
    converted_sequence_for_frame_3 = translate_dna_into_aminoacid_frame3(i)
    erev '  '+converted_sequence_for_frame_3+N+N
    if also_show_numbers
      verbose_report_numbered_amino_acid_sequence(converted_sequence_for_frame_3, '3')
    end
    e
    cliner
    if show_translations_aligned
      showorf(i) # Delegate into class Showorf here.
    end
  end
end

#show_all_dmp_files ⇒ Object

#

show_all_dmp_files

Show all .dmp files here.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2237

def show_all_dmp_files
  show_directory_content('.dmp')
end

#show_all_pathways ⇒ Object

#

show_all_pathways

Simply show all Pathways.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1439

def show_all_pathways
  ::Bioroebe::Pathways.show_all_pathways
end

#show_all_yaml_files ⇒ Object

#

show_all_yaml_files

We show which yaml files we will use here.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2380

def show_all_yaml_files
  erev 'The file that holds our restriction enzymes can be found here:'
  e
  erev "  #{sfile(::Bioroebe.restriction_enzymes_file)}"
  e
end

#show_alu_sequence ⇒ Object

#

show_alu_sequence

Invoke this method by doing something like:

alu_sequence?
#


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# File 'lib/bioroebe/shell/shell.rb', line 1495

def show_alu_sequence
  fasta_dataset = ::Bioroebe.parse_fasta(FILE_ALU_ELEMENTS)
  _ = fasta_dataset.fasta_sequence
  erev 'The ALU sequence in humans may be this (length: '+
        sfancy(_.size.to_s)+rev+'):'
  erev'  '+simp(_)
end

#show_aminoacid_sequence ⇒ Object

#

show_aminoacid_sequence

To show the aminoacid sequence, do:

show_aa
#


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# File 'lib/bioroebe/shell/shell.rb', line 10691

def show_aminoacid_sequence
  erev padding?+
       aminoacid_sequence? # aminoacids? # Will also use some padding.
end

#show_aminoacids_mass_table ⇒ Object Also known as: aminoacid_table_overview

#

show_aminoacids_mass_table

This shows the weight of the aminoacids, in a table-layout.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1428

def show_aminoacids_mass_table
  AminoacidsMassTable.report_which_file_is_used
  AminoacidsMassTable.show(padding?) # bl aminoacids_mass_table.rb
end

#show_aminoacids_residues ⇒ Object

#

show_aminoacids_residues

#


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# File 'lib/bioroebe/shell/shell.rb', line 1279

def show_aminoacids_residues
  _ = ''.dup
  _ << "#{rev}The aminoacid residues are:\n\n"
  ENGLISH_LONG_NAMES_FOR_THE_AMINO_ACIDS.each {|this_aminoacid|
    _ << this_aminoacid.ljust(14)+': '+
         simp(AMINO_ACIDS_RESTE[this_aminoacid.downcase])+N # Must downcase.
  }
  _ << N
  e _
end

#show_and_calculate_weight_of_dna_string(i = dna_sequence_object? ) ⇒ Object

#

show_and_calculate_weight_of_dna_string

#


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# File 'lib/bioroebe/shell/shell.rb', line 10144

def show_and_calculate_weight_of_dna_string(
    i = dna_sequence_object?
  )
  i = dna_sequence_object? if i.nil?
  i = dna_sequence_object? if is_a? Array and i.empty?
  sum = 0
  i.upcase.chars.each {|nucleotide|
    _ = case nucleotide
    when 'A'
      weight_of_adenin?
    when 'T'
      weight_of_thymin?
    when 'C'
      weight_of_cytosin?
    when 'G'
      weight_of_guanin?
    when 'U'
      weight_of_uracil?
    end
    sum += _.to_f
  }
  # ======================================================================= #
  # Round the sum properly here.
  # ======================================================================= #
  sum = sum.round(2)
  erev 'The weight of this nucleotide sequence ('+i.size.to_s+
       ' entries) is: '+
       simp(sum.to_s)+rev+' Dalton.'
end

#show_and_calculate_weight_of_dna_string_or_aminoacid_sequence(i = dna_sequence_object? ) ⇒ Object

#

show_and_calculate_weight_of_dna_string_or_aminoacid_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 2634

def show_and_calculate_weight_of_dna_string_or_aminoacid_sequence(
    i = dna_sequence_object?
  )
  if i.nil?
    if dna_sequence_object?
      i = dna_sequence_object?
    end
  end
  # ======================================================================= #
  # First, we check if the input is an aminoacid-sequence.
  # ======================================================================= #
  if ::Bioroebe.is_aminoacid?(i)
    reverse = AMINO_ACIDS_ENGLISH.reverse
    i = reverse[i] # Replace it with the one-letter code next.
    # ===================================================================== #
    # Obtain the mass of this aminoacid.
    # ===================================================================== #
    i = AMINO_ACIDS_AVERAGE_MASS_TABLE[i]
    erev 'The weight of this aminoacid is: '+
          simp(i.to_s)+rev+' Dalton.'
  else
    show_and_calculate_weight_of_dna_string(i)
  end
end

#show_available_vectors ⇒ Object

#

show_available_vectors

#


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# File 'lib/bioroebe/shell/shell.rb', line 7352

def show_available_vectors
  erev 'We will next try to show the available vectors.'
  erev 'For now, these are all file names that start with the '\
       'the prefix '+orange('vector_')+rev+'.'
  _ = return_available_vectors # Defined in bioroebe/shell.rb
  if _.empty?
    erev 'No vector-sequence was found.'
  else
    erev 'We found at the least one entry.'
    print '  '
    pp _
    erev 'Assigning the first one to the second sequence.'
    set_sequence_2(Bioroebe::Sequence.sequence_from_file(_.first))
    erev 'You can feedback this sequence via:'
    e
    erev '  seq2?'
    e
  end
end

#show_average_weight_of_a_nucleotide ⇒ Object

#

show_average_weight_of_a_nucleotide

The formulat was obtained from the following website:

http://www.biophp.org/minitools/useful_formulas/demo.php
#


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# File 'lib/bioroebe/shell/shell.rb', line 10182

def show_average_weight_of_a_nucleotide
  erev 'The average molecular weight (MW) of dsDNA is '+sfancy('660')+' Da.'
  erev 'The average molecular weight (MW) of ssDNA is '+sfancy('330')+' Da.'
end

#show_average_weight_of_an_aminoacid ⇒ Object

#

show_average_weight_of_an_aminoacid

Show the average weight for an aminoacid that is part of a protein.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8086

def show_average_weight_of_an_aminoacid
  erev "The average molecular weight (MW) of an "\
       "amino acid is #{sfancy('110')} Da."
end

#show_blosum_matrix ⇒ Object

#

show_blosum_matrix

Delegate towards bioroebe here, and invoke the .blosum() method.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5350

def show_blosum_matrix
  erev 'Showing the blosum matrix next:'
  require 'bioroebe/blosum/blosum.rb'
  Bioroebe::Blosum.show_matrix
end

#show_both_dna_strands ⇒ Object Also known as: show_double_strand

#

show_double_strand

#


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# File 'lib/bioroebe/shell/shell.rb', line 1799

def show_both_dna_strands
  show_main_sequence
  show_complement(string?, :include_prime_ends)
end

#show_ccaat_sites(search_for_this_sequence = 'CCAAT') ⇒ Object Also known as: show_CCAAT_sites

#

show_ccaat_sites

Use this method to locate CCAAT sites in the DNA string (the main string).

A CCAAT box, sometimes abbreviated a “CAAT box” or a “CAT box”, is a distinct pattern of nucleotides with the sequence “GGCCAATCT” or a sequence similar to that string.

This sequence usually occurs upstream by 60-100 bases to the initial transcription start site.

To test this method, you can try:

assign ATTTACGCGCCCGGCCAATCTGGCCGCGTACCCCCCCCCCGGCCAATCTATTTACGCGCCCGGCCAATCTGGCCGCGTACCCCCCCCCCGGCCAATCT; ccaat?
#


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# File 'lib/bioroebe/shell/shell.rb', line 5893

def show_ccaat_sites(
    search_for_this_sequence = 'CCAAT' # 'GGCCAATCT'
  )
  find_this_sequence(search_for_this_sequence)
  n_entries = raw_sequence?.scan("#{search_for_this_sequence}").size
  erev "The main sequence has #{simp(n_entries)}#{rev} CCAAT sites."
end

#show_chromosome_table ⇒ Object

#

show_chromosome_table

#


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# File 'lib/bioroebe/shell/shell.rb', line 7674

def show_chromosome_table
  lpadding_to_use = 16
  erev 'Chromosome Table from file '+sfile(FILE_CHROMOSOME_NUMBERS)+rev
  if File.exist? FILE_CHROMOSOME_NUMBERS
    dataset = YAML.load_file(FILE_CHROMOSOME_NUMBERS)
    e
    dataset.each_pair {|key, value|
      erev "  "+key.ljust(lpadding_to_use)+
           ' '+
           steelblue(value.to_s.rjust(3))
    }
    e
  else
    no_file_exists_at(FILE_CHROMOSOME_NUMBERS)
  end
end

#show_codon_piped_sequence ⇒ Object

#

show_codon_piped_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 1807

def show_codon_piped_sequence
  # _ = dna_sequence_object?.gsub(/(...)/, "\\1|") # Add | at every third position.
  # erev rev+padding?+leading_5_prime+sfancy(_)+rev+trailing_3_prime
  display_nucleotide_sequence(:default) { :piped }
end

#show_codon_table(i = nil) ⇒ Object

#

show_codon_table

#


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# File 'lib/bioroebe/shell/shell.rb', line 2499

def show_codon_table(i = nil)
  if i and i.is_a?(Array) and i.empty?
    i << 1 # Default to the vertebrate codon table in this case.
  end
  ShowThisCodonTable.new(i)
end

#show_codon_usage(i = dna_sequence_as_string? ) ⇒ Object

#

show_codon_usage

This shows the codon usage of the string.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4916

def show_codon_usage(
    i = dna_sequence_as_string?
  )
  if i.is_a? Array
    if i.empty?
      i = dna_sequence_as_string?
    else
      i = i.flatten.compact.join
    end
  end
  ::Bioroebe::ShowCodonUsage.new(i)
end

#show_codons_of_this_aminoacid_or_show_kazusa_codon(i = nil) ⇒ Object

#

show_codons_of_this_aminoacid_or_show_kazusa_codon

This method can be used to output which codon codes for a specific aminoacid.

The input to this method should be a specific codon, such as ATG or GGC and so forth.

If no input is provided, we will instead show the webpage of kazusa.

Invocation examples:

codon? ATG # => M
codon? AUG # => M
#


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# File 'lib/bioroebe/shell/shell.rb', line 2455

def show_codons_of_this_aminoacid_or_show_kazusa_codon(i = nil)
  if i.is_a? Array
    i = i.first
  end
  if i # If the user provided input, we check it.
    # ===================================================================== #
    # Next, find all codons for the given aminoacid.
    # ===================================================================== #
    e ::Bioroebe.codon_to_aminoacid(i)
  else
    erev "The URL is at: "\
         "#{simp('http://www.kazusa.or.jp/codon/')}"
  end
end

#show_commandline_options ⇒ Object

#

show_commandline_options

Show the available commandline options.

To invoke this method from the commandline, do:

bioroebe --help
#


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# File 'lib/bioroebe/shell/shell.rb', line 6224

def show_commandline_options
  e
  ecomment('  --silent               # perform a silent startup')
  ecomment('  --sequence             # use this nucleotide sequence on '\
           'startup; can be a number too such as 150')
  ecomment('  --n_fasta_entries      # report how many fasta '\
           'entries are in this directory')
  ecomment('  --disable-opn          # permanently disable opn')
  ecomment('  --random-aminoacids=33 # "generate" 33 random amino acids and display them')
  ecomment('  --n-aminoacids=33      # an alias to the ^^^ above')
  ecomment('  --protein-to-dna       # convert protein-aminoacid '\
           'sequence back to DNA')
  e
  erev 'Next some generic options will be shown. These may eventually'
  erev 'be moved into bin/bioroebe one day - but for now they will'
  erev 'be part of '+sfancy('Bioroebe::Shell')+'.'
  e
  erev 'The commandline interface for the java bindings can be found'
  erev 'at:'
  e
  efancy '  bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java'
  e
  e
  ecomment('  --create-jar           # This will package the .java specific '\
           'code into a .jar file.')
  e
  exit
end

#show_complement(i = dna_string?, , also_include_prime_ends = false) ⇒ Object

#

show_complement

If the second argument is true, we pad via 5’ and 3’.

As of Feb 2015, we will try with leading padding as well.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6943

def show_complement(
    i                       = dna_string?,
    also_include_prime_ends = false
  )
  case also_include_prime_ends
  # ======================================================================= #
  # === :show_leading_primes
  # ======================================================================= #
  when :show_leading_primes,
       :include_prime_ends
    also_include_prime_ends = true
  end
  i = dna_string? if i.nil?
  i = i.join('') if i.is_a? Array
  if also_include_prime_ends
    erev padding?+rev+
         leading_3_prime+
         sfancy(complement(i))+
         rev+trailing_5_prime
  else
    erev complement(i)
  end
end

#show_composition(i = dna_string? ) ⇒ Object

#

show_composition

This method will analyse the DNA string composition.

Invocation example:

scompo
#


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# File 'lib/bioroebe/shell/shell.rb', line 3723

def show_composition(
    i = dna_string?
  )
  length = i.size
  report_size_of_main_string
  hash = ::Bioroebe::CountAmountOfNucleotides.show_composition(i) # bl count_nucleotides
  erev 'Showing how many of the '+steelblue('four nucleotides')+rev+
       ' are in that sequence (absolute numbers):'
  print '  '
  string = ''.dup
  hash.each_pair {|nucleotide, n_times|
    string << "#{nucleotide}: #{lightslategray(n_times.to_s)}#{rev}, "
  }
  e string.rstrip.chop # .chop() to get rid of the last ',' token.
  erev "The respective frequencies derived from these absolute "\
       "numbers, #{steelblue('in percent')}#{rev}"\
       ", are:"
  print '  '
  hash.each_pair {|nucleotide, n_times|
    percentage = (n_times.to_f * 100 / length).round(2).to_s
    print "#{rev}#{nucleotide}: #{orange(percentage)}#{rev}% "
  }; erev
end

#show_config_dir ⇒ Object

#

show_config_dir

This method will show the configuration directory.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4591

def show_config_dir
  config_dir = File.dirname(__FILE__)+'/configuration/'
  erev 'The configuration directory for the Bioroebe::Shell is at:'
  erev '  `'+sfile(config_dir)+rev+'`'
end

#show_copyright_clause ⇒ Object

#

This method will simply show the licence used for the project.

This has to be updated manually, though; and since the licence may change one day, I will keep track when this method has been last modified, which is on the 28.04.2020 (28th April, 2020).

#


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# File 'lib/bioroebe/shell/shell.rb', line 6672

def show_copyright_clause
  e
  erev 'This project is free software, licensed under the LGPL-2.0 license.'
  erev 'No "any later clause"; LGPL-2.0 applies to it.'
  e
  erev '  Copyright: Robert A. Heiler (2010-2022 and later)'
  e
  erev 'The biomart component is licensed under the MIT license and is'
  erev 'written by Darren Oakley. The MIT license is retained for the'
  erev 'Biomart component.'
  e
  erev '(Note that the bioroebe project used to be under the GPL licence'
  erev 'before some time; see the homepage of this gem for the explanation'
  erev 'as to why a switch occurred towards LGPL.)'
end

#show_cpg_islands ⇒ Object

#

show_cpg_islands

Use this method to “search” for CpG islands in a sequence. These will then be highlighted, sort of.

To invoke this, try:

CG?
#


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# File 'lib/bioroebe/shell/shell.rb', line 6978

def show_cpg_islands
  display_nucleotide_sequence(main_sequence?.to_str) {{
    colourize_this_subsequence: 'CG'
  }}
end

#show_date ⇒ Object

#

show_date

#


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# File 'lib/bioroebe/shell/shell.rb', line 10681

def show_date
  erev Time.now.strftime('%d.%m.%Y')
end

#show_directory_content(of_this_dir = '*') ⇒ Object

#

show_directory_content

#


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# File 'lib/bioroebe/shell/shell.rb', line 1585

def show_directory_content(
    of_this_dir = '*'
  )
  of_this_dir.prepend '*' unless of_this_dir.include? '*'
  cliner {
    Dir[of_this_dir].sort.each_with_index {|entry, index|
      index += 1
      entry << '/' if File.directory?(entry)
      erev index.to_s.rjust(2)+') '+entry
    }
  }
end

#show_disulfides ⇒ Object

#

show_disulfides

Show the (possible) disulfide positions in a protein.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2045

def show_disulfides
  _ = aminoacid_sequence?
  if _.include? 'C'
    n_cytosines = _.count('C')
    erev "This aminoacid sequence has #{steelblue(n_cytosines.to_s)}#{rev} cysteines."
    if n_cytosines > 1
      erev 'Thus, there could be disulfide bonds. '+
           gold(cheerful_person)+rev
      show_sequence_with_a_ruler(:default, _)
      erev 'The positions of cysteines are at:'
      _.chars.each_with_index {|aminoacid, index|
        if aminoacid == 'C'
          erev 'Position: '+steelblue((index+1).to_s.rjust(3))
        end
      }
    end
  else
    e 'This aminoacid sequence has no cystein. Thus, '\
      'there can not be any disulfide bonds.'
  end
end

#show_dna_string(this_string = dna_string?, , truncate_too_long_result = do_truncate? ) ⇒ Object Also known as: show_main_string, report_sequence, show_sequence, show_main_dna_sequence, show_string

#

show_dna_string (show string tag, show tag)

Use this method to show the @sequence, or another string of your choosing, if you pass it to the method.

You can also invoke this method with something like this:

show_string { :with_colourized_separator }

This means that we will use ‘|’ separators that are colourized.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4498

def show_dna_string(
    this_string              = dna_string?,
    truncate_too_long_result = do_truncate?
  )
  result = rev.dup # This is the String that will be returned.
  case truncate_too_long_result
  when :do_not_truncate
    truncate_too_long_result = false
  end
  truncate_at_n_elements = TRUNCATE_AT_N_ELEMENTS
  if this_string.nil?
    this_string = dna_string? if dna_string?
  end
  if this_string.to_s.empty?
    report_that_a_string_must_be_assigned_first
  else
    # this_string.upcase! # Nope, do not upcase here. Use other methods to do so.
    if mode? == :dna
      if this_string.size > truncate_at_n_elements # Threshold for now.
        if truncate_too_long_result or
          (truncate_too_long_result == :do_not_truncate_and_do_not_show_leader_and_trailer)
          this_string =
            this_string[0, truncate_at_n_elements]+
            swarn(' [TRUNCATED as the sequence '\
            'is longer than '+truncate_at_n_elements.to_s+' nucleotides]')
        end
      end
      # =================================================================== #
      # Next, display the main string, without upcasing it.
      # =================================================================== #
      if block_given?
        yielded = yield
        case yielded
        when :with_colourized_separator
          _ = this_string.split(//)
          str = ''.dup
          _.each_with_index {|char, index|
            str << char
            str << paleturquoise('|')+sfancy if (index+1) % 3 == 0
          }
          this_string = str
        end
      end
      if truncate_too_long_result == :do_not_truncate_and_do_not_show_leader_and_trailer
      else
        result << padding?+leading_5_prime
      end
      # =================================================================== #
      # Next, add the DNA sequence to the result that will be displayed.
      # =================================================================== #
      result << colourize_dna_sequence(this_string)+rev
      if truncate_too_long_result == :do_not_truncate_and_do_not_show_leader_and_trailer
      else
        result << trailing_3_prime
      end
      # =================================================================== #
      # Delegate to class ShowNucleotideSequence next:
      # =================================================================== #
      display_nucleotide_sequence(this_string)
    else # Else use the aminoacid mode.
      show_aminoacid_sequence
    end
  end
end

#show_download_dir ⇒ Object

#

show_download_dir

#


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# File 'lib/bioroebe/shell/shell.rb', line 2344

def show_download_dir
  erev ::Bioroebe.download_directory?
end

#show_Ecoli_K12_information ⇒ Object

#

show_Ecoli_K12_information

#


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# File 'lib/bioroebe/shell/shell.rb', line 3077

def show_Ecoli_K12_information
  e
  erev 'Escherichia coli str. K-12 substr. MG1655, complete genome'
  e
  erev "  #{sfancy('https://www.ncbi.nlm.nih.gov/nuccore/NC_000913.3')}#{rev}"
  e
end

#show_editor_in_use ⇒ Object

#

show_editor_in_use

#


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# File 'lib/bioroebe/shell/shell.rb', line 7799

def show_editor_in_use
  e MAIN_EDITOR
end

#show_fasta_headers(i) ⇒ Object

#

show_fasta_headers

Just show the fasta headers.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5907

def show_fasta_headers(i)
  ::Bioroebe::ShowFastaHeaders.new(i) # Delegate into class Bioroebe::ShowFastaHeaders.
end

#show_fastq_quality_score_table(_ = Bioroebe.file_fastq_quality_schemes) ⇒ Object

#

show_fastq_quality_score_table

This method will output the FASTQ quality score table.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2677

def show_fastq_quality_score_table(
    _ = Bioroebe.file_fastq_quality_schemes
  )
  if File.exist? _
    erev 'Showing the dataset stored in '+sfile(_)+rev+' next:'
    e
    dataset = YAML.load_file(_)
    keys = dataset.keys
    keys.each {|this_key|
      e sfancy(this_key+':')
      e
      inner_dataset = dataset[this_key]
      erev '  ASCII character range: '+
           seagreen(inner_dataset['ascii_character_range'].to_s)
      erev '  Offset:                '+
           seagreen(inner_dataset['offset'].to_s)
      erev '  Quality score type:    '+
           seagreen(inner_dataset['quality_score_type'].to_s)
      erev '  Quality score range:   '+
           seagreen(inner_dataset['quality_score_range'].to_s)
      e
    }; e
  else
    erev 'No file exists at '+sfile(_)+rev+'.'
  end
end

#show_file_listing(from_this_directory = Dir.pwd) ⇒ Object

#

show_file_listing

Make use of DirectoryContent to show the content of a file.

To invoke this method from within the Bioroebe::Shell, do:

ll
#


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# File 'lib/bioroebe/shell/shell.rb', line 9645

def show_file_listing(
    from_this_directory = Dir.pwd
  )
  unless Object.const_defined?(:DirectoryParadise)
    begin
      require 'directory_paradise'
    rescue LoadError; end
  end
  _ = DirectoryParadise::Report.new(from_this_directory, :dont_run_yet)
  _.dont_report_total_filesize
  if run_as_GUI?
    _.disable_colours
  end
  _.disable_colours unless use_colours?
  _.run
end

#show_first_orf(of_this_sequence = dna_sequence_object? ) ⇒ Object

#

show_first_orf

This will show the first ORF.

Invocation example:

show_first_orf
#


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# File 'lib/bioroebe/shell/shell.rb', line 2397

def show_first_orf(
    of_this_sequence = dna_sequence_object?
  )
  _ = of_this_sequence
  return_all_possible_start_codons.each {|this_codon|
    if _.include? this_codon
      index = _.index(this_codon)
      sequence = _[index..-1]
      e rev+padding?+leading_5_prime+sfancy(sequence)+
        rev+trailing_3_prime+' (Start position at nucleotide: '+
        orange((index+1).to_s)+rev+')'
    else
      erev "Not found the codon #{simp(this_codon)}#{rev}."
    end
  }
end

#show_GFP_sequence ⇒ Object

#

show_GFP_sequence (gfp tag)

This method will show the GFP sequence, on the DNA level.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2951

def show_GFP_sequence
  erev return_five_prime_header+
       return_default_GFP_sequence
end

#show_header_of(i) ⇒ Object

#

show_header_of

#


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# File 'lib/bioroebe/shell/shell.rb', line 2928

def show_header_of(i)
  if i.is_a? Array
    i.each {|entry| show_header_of(entry) }
  else
    unless File.exist? i
      erev "No file exists at `#{sfile(i)}#{rev}`."
      return
    end
    case i
    # ===================================================================== #
    # === .pdb
    # ===================================================================== #
    when /\.pdb$/
      show_header_of_this_pdb_file(i)
    end
  end
end

#show_header_of_this_pdb_file(i) ⇒ Object

#

show_header_of_this_pdb_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 3855

def show_header_of_this_pdb_file(i)
  lines  = File.readlines(i)
  first  = lines.first.split(' ')[1..-1].join(' ').strip
  second = lines[1].split(' ')[1..-1].join(' ').strip
  erev first
  erev "  #{second}"
end

#show_help(optional_arguments = nil) ⇒ Object

#

show_help (help tag, he tag)

This is a wrapper over the class Help. For more documentation, please look at the class Bioroebe::BioShell::Help.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9623

def show_help(
    optional_arguments = nil
  )
  if run_in_GUI_mode?
    _ = ::Bioroebe::Shell::Help.new(:do_not_use_colours, :do_not_run_yet) { optional_arguments }
    _.build_help_string
    set_result(_.result?)
  else # This is the default for the commandline variant.
    ::Bioroebe::Shell::Help.new(use_colours?) { optional_arguments }
  end
end

#show_hint_how_to_use_the_local_sequences ⇒ Object

#

show_hint_how_to_use_the_local_sequences

Show a hint for the user.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2072

def show_hint_how_to_use_the_local_sequences
  unless return_fasta_files_in_the_log_directory.empty?
    erev 'You can load up any of these sequences by issuing:'
    e
    erev '  use_this_fasta 1 # for file number 1'
    e
  end
end

#show_histone_table ⇒ Object

#

show_histone_table

#


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# File 'lib/bioroebe/shell/shell.rb', line 7375

def show_histone_table
  erev 'The following table will show Calf Thymus Histones:'
  e
  erev 'Histone | number of residues | mass in kDa | n% Arginine | n% Lysine'
  erev '  H1             215               23.0          1             29'
  erev '  H2A            129               14.0          9             11'
  erev '  H2B            125               13.8          6             16'
  erev '  H3             135               15.3         13             10'
  erev '  H4             102               11.3         14             11'
  e
end

#show_history ⇒ Object

#

show_history (history tag)

Method to show the history.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8179

def show_history
  print_rev
  cliner {
    erev "Now showing the #{sfancy('history')}#{rev} of the BioShell:"
  }
  array_history = array_history?
  if array_history.empty?
    erev 'No input-history was used yet.'
  else
    result = ''.dup
    array_history.each_with_index {|item, index|
      index += 1
      result << ' - '.dup # Need to unfreeze the string.
      result << ' ' if array_history.size > 9 and index.to_s.size < 2
      result << '('+simp((index).to_s)+rev+') '+item.to_s+"\n"
    }
    erev result
  end
end

#show_how_to_use_the_names_for_the_taxonomy_table ⇒ Object

#

show_how_to_use_the_names_for_the_taxonomy_table

#


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# File 'lib/bioroebe/shell/shell.rb', line 7199

def show_how_to_use_the_names_for_the_taxonomy_table
  e 'We use these values for the names table:'
  e
  e '  taxid'
  e '  name_txt'
  e '  unique_name'
  e '  name_class'
  e
  e 'We will also try to show a random selection of 10 entries from '\
    'there now:'
  run_sql 'SELECT taxid,name_txt,unique_name,name_class FROM names 
    ORDER BY RANDOM(), taxid LIMIT 10'
end

#show_html_colours ⇒ Object

#

show_html_colours

#


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# File 'lib/bioroebe/shell/shell.rb', line 2279

def show_html_colours
  e 'The available HTML colours are:'; e
  ::Colours.show_html_colours; e
end

#show_human_genome_version(remote_URL = 'https://www.ensembl.org/Homo_sapiens/Info/Index') ⇒ Object

#

show_human_genome_version

Use this method to show the most current human genome version.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1448

def show_human_genome_version(
    remote_URL = 'https://www.ensembl.org/Homo_sapiens/Info/Index'
  )
  human_genome_version = '' # Default.
  dataset = URI.open(remote_URL).read
  use_this_regex = /Genome assembly: (.{1,11}\.p\d+) <small>/ # See: https://rubular.com/r/DD5FhaPs3b
  scanned = dataset.scan(use_this_regex).flatten
  human_genome_version = scanned.first.to_s
  _ = "#{rev}The most current human genome version is: "\
      "#{sfancy(human_genome_version)}\n".dup
  _ << "The URL that was used to query this has been: "\
       "#{steelblue(remote_URL)}"
  e _
end

#show_hydropathy_table ⇒ Object

#

show_hydropathy_table

Show the hydropathy table.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1032

def show_hydropathy_table
  e
  HYDROPATHY_TABLE.each_pair {|aminoacid_one_letter, hydropathy_value|
    e '  '+sfancy(aminoacid_one_letter)+'  | '+
      simp(hydropathy_value.to_s.rjust(4))
  }; e
end

#show_information_about_the_gff_format ⇒ Object

#

show_information_about_the_gff_format

#


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# File 'lib/bioroebe/shell/shell.rb', line 7875

def show_information_about_the_gff_format
  erev 'Fields must be tab-separated in the .gff format.'
  e
  erev 'All but the final field in each feature line must'
  erev 'contain a value; "empty" columns should be denoted with a "."'
  e
  egold 'seqname:'
  erev 'This is the name of the chromosome or scaffold; chromosome names'
  erev 'can be given with or without the "chr" prefix.'
  erev 'Important note: the seqname must be one used within Ensembl, '
  erev 'i.e. a standard chromosome name or an Ensembl identifier such as a'
  erev 'scaffold ID, without any additional content such as species or'
  erev 'assembly. See the example GFF output below.'
  e
  egold 'source:'
  erev 'Name of the program that generated this feature, or '
  erev 'the data source (database or project name)'
  e
  egold 'feature:'
  erev 'feature type name, e.g. Gene, Variation, Similarity'
  e
  egold 'start:'
  erev 'Start position of the feature, with sequence numbering starting at 1.'
  e
  egold 'end:'
  erev 'End position of the feature, with sequence numbering '\
       'starting at 1.'
  e
  egold 'score:'
  erev 'A floating point value.'
  e
  egold 'strand:'
  erev 'defined as + (forward) or - (reverse).'
  e
  egold "frame:"
  erev " - One of '0', '1' or '2'. '0' indicates that the first base "
  erev "of the feature is the first base of a codon, '1' that the second "
  erev "base is the first base of a codon, and so on."
  e
  egold 'attribute:'
  erev 'A semicolon-separated list of tag-value pairs, providing '
  erev 'additional information about each feature.'
  e
end

#show_insulin_entries_at_NCBI ⇒ Object

#

show_insulin_entries_at_NCBI

#


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# File 'lib/bioroebe/shell/shell.rb', line 757

def show_insulin_entries_at_NCBI
  e
  e 'https://www.ncbi.nlm.nih.gov/gene/3630'
  e 'https://www.ncbi.nlm.nih.gov/nuccore/NM_000207.3'
  e 'https://www.ncbi.nlm.nih.gov/protein/NP_000198.1'
  e
end

#show_jumper_directories ⇒ Object

#

show_jumper_directories

#


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# File 'lib/bioroebe/shell/shell.rb', line 9928

def show_jumper_directories
  if @internal_hash[:array_jumper_directories].empty?
    erev 'No jumper directory has been assigned yet.'
  else
    erev 'The available jumper directories are:'
    pp @internal_hash[:array_jumper_directories]
  end
end

#show_known_nls_sequences ⇒ Object

#

show_known_nls_sequences

This Wikipedia page may be useful:

https://en.wikipedia.org/wiki/Nuclear_localization_sequence
#


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# File 'lib/bioroebe/shell/shell.rb', line 1048

def show_known_nls_sequences
  erev "These NLS sequences are known:#{N}#{N}"
  padding = 36
  NUCLEAR_LOCALIZATION_SEQUENCES.each_pair {|key, value|
    e sfancy(key.ljust(padding))+' '+value
  }
end

#show_last_downloaded_file ⇒ Object

#

show_last_downloaded_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 4600

def show_last_downloaded_file
  if array_all_downloads?.empty?
    erev 'We have not yet downloaded any file.'
  else
    erev 'The last downloaded data was: '+
          sfancy(array_all_downloads?.last)
  end
end

#show_last_input ⇒ Object

#

show_last_input

sli can be used as command to access this method.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4105

def show_last_input
  if readline_is_available?
    e sfancy(Readline::HISTORY[-1])
    Readline::HISTORY.pop
  end
  e "The last user input was: #{sfancy(user_input?)}"
end

#show_length_of_alpha_helix(i) ⇒ Object

#

show_length_of_alpha_helix

#


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# File 'lib/bioroebe/shell/shell.rb', line 1272

def show_length_of_alpha_helix(i)
  erev ::Bioroebe::AlphaHelix.length?(i)
end

#show_local_sequences ⇒ Object

#

show_local_sequences

This method will show the available local sequences.

#


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# File 'lib/bioroebe/shell/shell.rb', line 9818

def show_local_sequences
  possible_matches = return_fasta_files_in_the_log_directory
  if possible_matches.empty?
    erev 'No local fasta sequences could be found.'
  else
    e
    erev 'The following local sequences were found in '\
         'the main log'
    erev 'directory ('+sdir(log_dir?)+rev+').'
    e
    possible_matches.each_with_index {|entry, index|
      index += 1
      _ = possible_matches.size.to_s.size
      erev padding?+'('+index.to_s.rjust(_)+') '+rev+
           sfile(File.basename(entry))+rev
    }; e
  end
end

#show_log_dir ⇒ Object

#

show_log_dir

#


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# File 'lib/bioroebe/shell/shell.rb', line 3848

def show_log_dir
  e ::Bioroebe.log_dir?
end

#show_mnemo ⇒ Object

#

show_mnemo

A little helper-method to memorize things.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4034

def show_mnemo
  e
  erev 'Amino Acids with negatively charged side groups: -'
  e sfancy('  D E')
  erev 'Amino Acids with positive charged side groups: +'
  e sfancy('  K R H')
  e
  e sfancy('Oxidoreduktasen:')+rev+' Oxidations-Reduktions-Reaktionen'
  e sfancy('Transferasen:')+rev+'    Übertragung funktioneller Gruppen'
  e sfancy('Hydrolasen:')+rev+'      Hydrolasereaktionen'
  e sfancy('Lyasen:')+rev+'          Eliminierung von Gruppen unter '\
    'Ausbildung von Doppelbindungen'
  e sfancy('Isomerasen:')+rev+'      Isomerisierungen'
  e sfancy('Ligasen:')+rev+'         ATP-hydrolytic formation of bonds'
  e
end

#show_molweight(use_cliner = true) ⇒ Object

#

show_molweight

#


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# File 'lib/bioroebe/shell/shell.rb', line 4746

def show_molweight(
    use_cliner = true
  )
  cliner if use_cliner
  MolecularWeightOfNucleotides.weights.each_with_index {|entry, index|
    case index
    when 0
      erev 'Adenine:  '+sfancy(entry.to_s)+rev
    when 1
      erev 'Thymine:  '+sfancy(entry.to_s)+rev
    when 2
      erev 'Guanine:  '+sfancy(entry.to_s)+rev
    when 3
      erev 'Cytosine: '+sfancy(entry.to_s)+rev
    end
  }; cliner if use_cliner
end

#show_my_fasta_file ⇒ Object

#

show_my_fasta_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 2287

def show_my_fasta_file
  e HOME_DIRECTORY_OF_USER_X+
    'data/science/BIOINFORMATIK/data/FASTA/tardigrada_fasta.ffn'
end

#show_name_of_the_gene ⇒ Object

#

show_name_of_the_gene

#


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# File 'lib/bioroebe/shell/shell.rb', line 4703

def show_name_of_the_gene
  erev 'The name of the gene at hand is: '+
        sfancy(sequence_object?.name_of_gene)
end

#show_nucleotide_sequence? ⇒ Boolean Also known as: display_nucleotide_object?

#

show_nucleotide_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 9840

def show_nucleotide_sequence?
  @internal_hash[:show_nucleotide_sequence]
end

#show_nucleotides_table ⇒ Object

#

show_nucleotides_table

Use this method to show the nucleotides table - their formula and the molecular mass.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1469

def show_nucleotides_table
  array_display_these = %w(
    Adenin Cytosin Guanin Thymin
  )
  # ======================================================================= #
  # Grab the nucleotides.yml dataset next
  # ======================================================================= #
  dataset = YAML.load_file(FILE_NUCLEOTIDES)
  dataset.each_pair {|key, chemical_formula|
    if array_display_these.include? key # Display it in this case.
      molmasse = ChemistryParadise::CalculateAtomicMass.new(chemical_formula, :do_not_report).masse?
      molmasse = molmasse.to_f.round(2)
      e key.to_s.ljust(8)+' -> '+chemical_formula.to_s.rjust(8)+
        rev+' (Molecular mass: '+simp(molmasse.to_s)+')'+rev
    end
  }
end

#show_numbered_nucleotide_positions(_ = sequence?.string?) ⇒ Object

#

show_numbered_nucleotide_positions

This method will show “numbered” nucleotide positions such as:

1234567891234567891234567
ATGCAGGTCATCAGTCAGTCAGTCA
#


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# File 'lib/bioroebe/shell/shell.rb', line 7812

def show_numbered_nucleotide_positions(
    _ = sequence?.string?
  )
  chars = _.chars
  chunk = chars.each_slice(40) 
  chunked = chunk.map {|line| line.join }
  chunked.each {|line|
    chars = line.chars
    upper_strand = ''.dup
    counter = 0
    chars.each {|char| counter += 1
      if counter > 9
        counter = 0
      end
      upper_strand << counter.to_s
    }
    e lightsteelblue(upper_strand)
    erev line
  }
end

#show_oligo_length_three(sequence = dna_sequence_object? ) ⇒ Object

#

show_oligo_length_three

We align in chunks of three and tell the user how often we can find these individual codons.

Invocation example:

random 99; oligo_3
#


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# File 'lib/bioroebe/shell/shell.rb', line 10746

def show_oligo_length_three(
    sequence = dna_sequence_object?
  )
  sequence = sequence.upcase # This is the sequence that will be scanned.
  dna = ::Bioroebe.dna? # This is equal to A, T, C and G.
  erev 'We will align the nucleotides in chunks of 3 and show their '\
       'frequency.'
  dna.each {|first_entry| # First nucleotide.
    dna.each {|second_entry| # Second nucleotide.
      dna.each {|third_entry| # Third nucleotide.
        _ = first_entry+second_entry+third_entry
        erev _+' '+sequence.scan(_).size.to_s
      }
    }
  }
end

#show_oligo_length_two(string = string? ) ⇒ Object

#

show_oligo_length_two

Show all oligo of length two.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1911

def show_oligo_length_two(
    string = string?
  )
  sequence = string.upcase # Shorter copy and always upcased.
  dna = ::Bioroebe.dna?
  dna.each {|first_entry|
    dna.each {|second_entry|
      _ = "#{first_entry}#{second_entry}"
      erev _+' '+sequence.scan(_).size.to_s
    }
  }
end

#show_ori_sequences ⇒ Object

#

show_ori_sequences

The DnaA box is: TTATC[CA]AA

#


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# File 'lib/bioroebe/shell/shell.rb', line 8259

def show_ori_sequences
  erev 'The DnaA box has this consensus sequence: '+
        sfancy("5'-TTATC[CA]A[CA]A-3'")
  _ = 'TTATCCACA'
  erev 'Searching for '+_
  try_to_find_restriction_enzymes_for(_)
  _ = 'TTATCAAAA'
  erev 'Searching for '+_
  try_to_find_restriction_enzymes_for(_)
end

#show_position_for_the_main_sequence ⇒ Object

#

show_position_for_the_main_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 1927

def show_position_for_the_main_sequence
  array = sequence?.scan(/.{,25}/)
  index_position = 1
  array.each {|entry|
    unless entry.empty?
      erev entry.split(//).join('   ')
      second_line = ''
      start = index_position
      index_position += entry.size
      start.upto(index_position-1) {|position|
        second_line << position.to_s.ljust(4)
      }
      erev cadetblue(second_line)+rev
      e
    end
  }
end

#show_position_of_sequence(i = aa_sequence?, , chunk_size = 10) ⇒ Object

#

show_position_of_sequence

This currently works only for Amino Acids - at the least I have tested it only on aminoacids so far, and not on DNA/RNA.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7279

def show_position_of_sequence(
    i          = aa_sequence?,
    chunk_size = 10 # How many chunks to display per row.
  )
  array = i.chars
  _ = ''.dup # The Display-String.
  index_string = ''
  0.upto(array.size) {|index|
    _ << array[index].to_s.rjust(2)+' '
    unless array.size == index
      index_string << palevioletred((index+1).to_s.rjust(2)+' ')
    end
    if index % chunk_size == (chunk_size - 1)
      _ << N
      _ << index_string << rev << N << N
      index_string = ''
    end
  }
  erev _ # Report it finally.
  erev index_string
end

#show_possible_codons_for_this_aminoacid(i) ⇒ Object

#

show_possible_codons_for_this_aminoacid

#


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# File 'lib/bioroebe/shell/shell.rb', line 10671

def show_possible_codons_for_this_aminoacid(i)
  possible_codons = PossibleCodonsForThisAminoacid[i,
    :use_only_the_four_standard_nucleotide_letters]
  array_aminoacid_sequence? << possible_codons
  return possible_codons
end

#show_possible_phosphorylation_sites(i = aminoacid_sequence?) ) ⇒ Object

#

show_possible_phosphorylation_sites

This method will find all possible phosphorylation sites in any given target sequence. It will also identify the aminoacids that can be phosphorylated.

To test this, try:

random 250; P?
#


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# File 'lib/bioroebe/shell/shell.rb', line 10585

def show_possible_phosphorylation_sites(i = aminoacid_sequence?)
  _ = dna_sequence_object?
  array_all_codons = []
  array_all_codons << ::Bioroebe.codons_for?(:serine)
  array_all_codons << ::Bioroebe.codons_for?(:tyrosine)
  array_all_codons << ::Bioroebe.codons_for?(:threonine)
  array_all_codons.flatten!
  # ======================================================================= #
  # === Convert Y into Purine/Pyrimidine next
  # ======================================================================= #
  if array_all_codons.any? {|entry| entry.end_with? 'Y' }
    array_all_codons.map! {|inner_entry|
      if inner_entry.end_with? 'Y'
        inner_entry = [
          inner_entry.sub(/Y$/,'T'),
          inner_entry.sub(/Y$/,'C')
        ]
      end
      inner_entry
    }
    array_all_codons.flatten!
  end
  all_codons_found_in_the_sequence = []
  n_phosphorylation_sites = 0
  n_phosphorylation_sites = 
    array_all_codons.map {|entry|
      if _.scan(/#{entry}/).size > 0
        all_codons_found_in_the_sequence << entry
      end
      _.scan(/#{entry}/).size  }.inject(0){|sum, inner_element| sum + inner_element
    }
  all_codons_found_in_the_sequence.uniq!
  singular_or_plural = 'site'
  if n_phosphorylation_sites < 1
    singular_or_plural << 's'
  end
  erev 'In this sequence, we have found '+simp(n_phosphorylation_sites.to_s)+rev+
       ' possible phosphorylation '+singular_or_plural+', using all '\
       '3 possible frames.'
  e
  erev 'In particular, these '+all_codons_found_in_the_sequence.size.to_s+
       ' different codons were found: '
  e
  erev '  '+simp(all_codons_found_in_the_sequence.join('/'))+rev
  e
  erev 'For the first frame, the start positions are these:'
  e
  # ======================================================================= #
  # === Find the start positions for frame 1 next
  # ======================================================================= #
  array_start_positions_for_frame_1 = []
  scanned_result = _.scan(/.../)
  scanned_result.each_with_index {|codon, index|
    if all_codons_found_in_the_sequence.include? codon
      array_start_positions_for_frame_1 << (index * 3)+1
    end
  }
  erev '  DNA:     '+simp(array_start_positions_for_frame_1.join('/'))+rev
  erev '  Protein: '+simp(array_start_positions_for_frame_1.map {|entry|
    entry = entry.to_i * 3
    entry.to_s
  }.join('/'))+rev
  # ======================================================================= #
  # Now modify the DNA sequence there but only in the first frame.
  # ======================================================================= #
  new_colourized_dna_sequence = ''
  all_triplets = _.scan(/.../)
  all_triplets.each {|codon|
    codon = swarn(codon) if all_codons_found_in_the_sequence.include? codon
    new_colourized_dna_sequence << codon+rev
  }
  e
  erev 'The DNA sequence with possible phosphorylation sites is:'
  e
  erev left_padding?+leading_five_prime+new_colourized_dna_sequence+trailing_three_prime
  e
  erev 'The Aminoacid sequence with possible phosphorylation sites is:'
  e
  erev '  '+
       ::Bioroebe.colourize_aa(i, ARRAY_AMINOACIDS_THAT_CAN_BE_PHOSPHORYLATED).to_s
  e
end

#show_protein_composition(i) ⇒ Object

#

show_protein_composition

Delegate towards class CountAmountOfAminoacids

#


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# File 'lib/bioroebe/shell/shell.rb', line 5271

def show_protein_composition(i)
  ::Bioroebe::CountAmountOfAminoacids.new(i) # bl $BIOROEBE/count_amount_of_aminoacids.rb
end

#show_readline_completions ⇒ Object

#

show_readline_completions

#


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# File 'lib/bioroebe/shell/readline.rb', line 82

def show_readline_completions
  e 'The available completions are:'
  e
  pp ARRAY_WITH_COMPLETIONS
  e
end

#show_resources_about_the_horseradish_peroxidase ⇒ Object

#

show_resources_about_the_horseradish_peroxidase

#


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# File 'lib/bioroebe/shell/shell.rb', line 1574

def show_resources_about_the_horseradish_peroxidase
  e
  e 'https://www.ncbi.nlm.nih.gov/gene/?term=%22Horseradish+Peroxidase%22'
  e 'https://www.ncbi.nlm.nih.gov/gene/836533'
  e 'Fasta: https://www.ncbi.nlm.nih.gov/nuccore/NC_003076.8?report=fasta&from=25659257&to=25661007&strand=true'
  e
end

#show_reste ⇒ Object

#

show_reste

This will show the residues of the various amino acids.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10192

def show_reste
  e; AMINO_ACIDS_RESTE.each_pair {|key, value|
    erev '  '+key.ljust(14)+' -> '+sfancy(value)
  }; e
end

#show_restriction_enzymes(optional_input = nil) ⇒ Object

#

show_restriction_enzymes

Display the available restriction enzymes here.

If we pass an argument, then we assume that we wish to show only these restriction enzymes that cut at n bp.

Invocation example:

show_restriction_enzymes(:show_all)
#


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# File 'lib/bioroebe/shell/shell.rb', line 9059

def show_restriction_enzymes(optional_input = nil)
  case optional_input
  when nil, :show_all # This means to show everything.
    ::Bioroebe.show_restriction_enzymes # Defined in module_methods.rb
  else # Ok we gave input then.
    _ = ::Bioroebe.restriction_enzymes
    _.select! {|entry|
      last = entry.last
      last = last.split(' ').last
      if last == optional_input
        true
      else
        false
      end
    }
    if _.empty?
      erev 'We found no match for '+optional_input+'.'
    else # else display the cutters.
      erev 'These enzymes cut at `'+sfancy(optional_input)+rev+'` nucleotides.'
      _.each {|entry|
        entry[0] = entry[0].rjust(15)
        entry[1] = entry[1].gsub(/ (.+)/, swarn(' \\1')+rev)
        e "  #{entry.join(' -> ')}"
      }
      erev 'These are '+simp(_.size.to_s)+rev+' restriction enzymes.'
    end
  end
end

#show_restriction_table ⇒ Object

#

show_restriction_table

This method will show a restriction table, that is, a table with some different restriction enzymes.

To invoke this method, do:

show_restriction_table
#


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# File 'lib/bioroebe/shell/shell.rb', line 2887

def show_restriction_table
  most_ljust = 20
  _ = ''.dup
  _ << 'Showing a few different cutters (4,5,6,7,8) in table format next:'+N
  _ << '---------------------------------------------------------'+N
  _ << peru('  4-cutter'.ljust(most_ljust))+' | '+orange('ChaI'.ljust(10))+' | '+
       olivedrab('GATC'.ljust(10))+N
  _ << peru('  5-cutter'.ljust(most_ljust))+' | '+orange('FmuI'.ljust(10))+' | '+
       olivedrab('GGNCC'.ljust(10))+N
  _ << peru('  6-cutter'.ljust(most_ljust))+' | '+orange('EcoRI'.ljust(10))+' | '+
       olivedrab('GAATTC'.ljust(10))+N
  _ << peru('  7-cutter'.ljust(most_ljust))+' | '+orange('PfoI'.ljust(10))+' | '+
       olivedrab('TCCNGGA'.ljust(10))+N
  _ << peru('  8-cutter'.ljust(most_ljust))+' | '+orange('PacI'.ljust(10))+' | '+
       olivedrab('TTAATTAA'.ljust(10))+N
  _ << '---------------------------------------------------------'+N
  erev _
end

#show_reverse_dna_string ⇒ Object

#

show_reverse_dna_string

This method will simply show the DNA sequence reversed.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2333

def show_reverse_dna_string
  erev padding?+
       leading_five_prime+
       sfancy(return_reverse_dna_string)+
       rev+
       trailing_three_prime
end

#show_rna_sequence(i = sequence_object?.to_rna) ⇒ Object

#

show_rna_sequence

Use this method to convert a given sequence to RNA.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2511

def show_rna_sequence(
    i = sequence_object?.to_rna
  )
  i = sequence_object?.to_rna if i.nil?
  i = i.to_str if i.respond_to? :to_str
  if i.include? 'T'
    i.tr!('T','U')
  end
  display_nucleotide_object?.display(i) {{ use_this_as_padding: lpad? }}
end

#show_save_file ⇒ Object

#

show_save_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 1562

def show_save_file
  result = <<-EOF
#{rev}We will store into the file #{sfile(save_file?)}#{rev}.
#{rev}If you wish to instead store into the current directory,
#{rev}input "save_here".
EOF
  e result
end

#show_segments ⇒ Object

#

show_segments

This method will show the DNA segments via a R-compatible way.

Usage example:

set AAAATGCAGTAACCCATGCCC; show_segments
#


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# File 'lib/bioroebe/shell/shell.rb', line 10561

def show_segments
  array = ::Bioroebe.scan_this_input_for_startcodons(dna_sequence_object?)
  erev '         start end width'
  array.each_with_index {|inner_array, index|
    index += 1
    start_position = inner_array.first
    codon          = inner_array.last.first
    erev '  ['+index.to_s+']  '+start_position.to_s.rjust(5)+' '+
          (start_position+2).to_s.rjust(5)+' '+'3'.rjust(4)+' ['+codon.downcase+']'
  }
end

#show_seq_1(i = seq1?) ) ⇒ Object

#

show_seq_1

#


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# File 'lib/bioroebe/shell/shell.rb', line 10509

def show_seq_1(i = seq1?)
  erev padding?+leading_five_prime+
       sfancy(i)+rev+trailing_three_prime
end

#show_seq_2(i = seq2?) ) ⇒ Object

#

show_seq_2

#


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# File 'lib/bioroebe/shell/shell.rb', line 10517

def show_seq_2(i = seq2?)
  erev padding?+leading_five_prime+
       sfancy(i)+rev+trailing_three_prime
end

#show_seq_3(i = seq3?) ) ⇒ Object

#

show_seq_3

#


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# File 'lib/bioroebe/shell/shell.rb', line 10525

def show_seq_3(i = seq3?)
  erev padding?+leading_five_prime+
       sfancy(i)+rev+trailing_three_prime
end

#show_seq_4 ⇒ Object

#

show_seq_4

#


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# File 'lib/bioroebe/shell/shell.rb', line 10533

def show_seq_4
  erev padding?+leading_five_prime+sfancy(seq4?)+rev+trailing_three_prime
end

#show_seq_5 ⇒ Object

#

show_seq_5

#


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# File 'lib/bioroebe/shell/shell.rb', line 10540

def show_seq_5
  erev padding?+leading_five_prime+sfancy(seq5?)+rev+trailing_three_prime
end

#show_seq_6 ⇒ Object

#

show_seq_6

#


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# File 'lib/bioroebe/shell/shell.rb', line 10547

def show_seq_6
  erev padding?+leading_five_prime+sfancy(seq6?)+rev+trailing_three_prime
end

#show_sequence_in_splitted_form(how_many = 3, use_this_token_for_rejoining = ' ') ⇒ Object

#

show_sequence_in_splitted_form

We will show the main DNA sequence in a three-letter splitted form.

You can optionally use an argument, the first argument, a number. By default this is 3, so we will split into chunks of 3.

The second argument says which token we will use for rejoining. It defaults to ‘ ’ so the nucleotides will be rejoined via ‘ ’, but you can also use another token such as ‘-’, which may lead to a String such as ‘ATG-CGA-ACC’ and so forth.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1988

def show_sequence_in_splitted_form(
    how_many                     = 3,
    use_this_token_for_rejoining = ' ' # <- Which token to use for the re-joining action.
  )
  case how_many
  when nil, :default # Use a default value here.
    how_many = 3
  end
  result = '.' * how_many.to_i
  use_this_regex = /#{result}/
  if string?.empty?
    erev 'Please first "assign" a sequence.'
  else
    if block_given?
      yielded = yield
      if yielded.is_a? Hash
        # ================================================================= #
        # === :use_this_token
        # ================================================================= #
        if yielded.has_key? :use_this_token
          use_this_token_for_rejoining = yielded.delete(:use_this_token)
        end
      end
    end
    string = string?.to_s
    scanned = string.scan(use_this_regex)
    scanned.map! {|entry|
      # =================================================================== #
      # Colourize start codons next.
      # =================================================================== #
      if is_this_a_start_codon? entry
        entry = mediumseagreen(entry)+
                return_colour_for_nucleotides
      elsif is_this_a_stop_codon? entry
        entry = mediumorchid(entry)+
                return_colour_for_nucleotides
      end
      entry
    }
    _ = scanned.join(use_this_token_for_rejoining)
    # ===================================================================== #
    # Finally show the sequence.
    # ===================================================================== #
    erev left_padding?+
         five_prime+
         return_colour_for_nucleotides+
         _+
         rev+
         three_prime
  end
end

#show_sequence_with_a_ruler(group_together_n_nucleotides = :default, use_this_sequence = main_sequence?, , type = type? ) ⇒ Object

#

show_sequence_with_a_ruler

This will show the main sequence together with a “ruler” on top.

The first argument specifies how many nucleotides are to be displayed per given line.

This method can also be called in this way:

show_sequence_with_a_ruler { :without_colours }

This will skip showing the ruler.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4829

def show_sequence_with_a_ruler(
    group_together_n_nucleotides = :default,
    use_this_sequence            = main_sequence?,
    type                         = type?
  )
  case use_this_sequence
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    use_this_sequence = main_sequence?
  end
  if group_together_n_nucleotides.is_a?(Array)
    group_together_n_nucleotides = group_together_n_nucleotides.first
    if group_together_n_nucleotides.nil? or group_together_n_nucleotides.empty?
      group_together_n_nucleotides = :default
    end
  end
  case group_together_n_nucleotides
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default,
       nil
    group_together_n_nucleotides = 70
  end
  if group_together_n_nucleotides.is_a? String
    # ===================================================================== #
    # We need an Integer here.
    # ===================================================================== #
    group_together_n_nucleotides = group_together_n_nucleotides.to_i
  end
  e
  msg = "Displaying the main sequence (length: #{use_this_sequence.to_s.size}) "\
        "in a chunk of #{slateblue(group_together_n_nucleotides.to_s)}#{rev}\n".dup 
  case type
  when :dna
    msg << "nucleotides"
  when :aminoacids
    msg << "aminoacids"
  end
  msg << " next."
  e msg
  e
  use_this_sequence = use_this_sequence.to_s
  chunks = use_this_sequence.split(/(.{#{group_together_n_nucleotides}})/).reject(&:empty?)
  array = chunks.each_slice(group_together_n_nucleotides).to_a.flatten #.join.split("\n")
  use_this_ruler_type = :show_ruler # Note that :show_ruler is the default.
  # ======================================================================= #
  # === Handle blocks given next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :without_colours
    # ===================================================================== #
    when :without_colours
      use_this_ruler_type = :without_colours
    end
  end
  array.each {|sequence|
    show_nucleotide_sequence?.display_with_prior_formatting(sequence) {
      use_this_ruler_type
    }
    e
  }
end

#show_sigma_tutorial ⇒ Object

#

show_sigma_tutorial

This method tells the user a bit about the sigma factors.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4068

def show_sigma_tutorial
  erev 'This subsection contains some information about Sigmafactors.'
  e
  erev 'A sigma factor a protein needed for initiation of RNA synthesis.'
  e
  erev 'It is a bacterial transcription initiation factor.'
  e
  erev 'It will enable the specific binding of RNA polymerase to gene promoters.'
  e
  erev 'Sigma factors vary, which allows the bacterial cell to respond to'
  erev 'different environmental signals.'
  e
  erev 'Every molecule of RNA polymerase holoenzyme will contain only one '\
       'sigma factor.'
  e
  erev 'The number of sigma factors varies between bacterial species.'
  e
  erev 'E. coli has seven sigma factors.'
  e
  erev 'Sigma factors are distinguished by their characteristic molecular '\
       'weights.'
  e
  erev 'For instance, sigma-70 refers to the sigma factor with a molecular '\
       'weight of 70 kDa.'
  e
  erev 'Once initiation of RNA transcription is complete, the sigma'
  erev 'factor can leave the complex.'
  e
  erev 'Sigmafactor rpoD 70 can be found here:'
  e '  '+simp('http://www.ncbi.nlm.nih.gov/gene/947567')
end

#show_sixpack_alignment(i = dna_sequence_object? ) ⇒ Object

#

show_sixpack_alignment

We will feed some input to class Bioroebe::SimpleStringComparer.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10204

def show_sixpack_alignment(
    i = dna_sequence_object?
  )
  erev 'Input sequence 1:'
  string1 = $stdin.gets.chomp
  erev 'Input sequence 2:'
  string2 = $stdin.gets.chomp
  # ======================================================================= #
  # Delegate into class SimpleStringComparer next.
  # ======================================================================= #
  _ = ::Bioroebe::SimpleStringComparer.new(:dont_run_yet) # bl $BIOROEBE/string_matching/simple_string_comparer.rb
  _.set_main_alignment_token_to '|'
  _.string1 = string1
  _.string2 = string2
  _.compare
end

#show_start_and_stop_codons ⇒ Object

#

show_start_and_stop_codons

This will show BOTH start and stop codons, in different colours.

Since start codons may be more important, we will first locate and colourize them, and afterwards, will also colourize the stop codons.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7842

def show_start_and_stop_codons
  _ = string?
  start_codon = ::Bioroebe.start_codon?
  stop_codons = ::Bioroebe.stop_codons?
  _.gsub!(/(#{start_codon})/, yellow+'\\1'+colour_for_nucleotide)
  stop_codons.each {|stop_codon|
    _.gsub!(/(#{stop_codon})/, salmon('\\1')+colour_for_nucleotide)
  }
  erev 'Start codon: '+yellow+start_codon+rev
  stop_codons = stop_codons.join(', ').strip
  stop_codons.chop! if stop_codons.end_with? ','
  # ======================================================================= #
  # Show the stop codons that we will use:
  # ======================================================================= #
  erev 'Stop codons: '+salmon(stop_codons)+rev
  erev dna_padding(_)
end

#show_startup_information ⇒ Object

#

show_startup_information

This method here will usually be shown only once, on an initial startup of the Bioroebe::Shell. Afterwards, it will no longer be shown at all.

Note that showing this can be disabled.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7740

def show_startup_information
  e
  erev "This seems to be the first time that you are using the "\
       "#{olivedrab('Bioroebe::Shell')}#{rev}, at the least on"
  erev 'this computer.'
  e
  erev 'It is recommended to have a look at the following components first:'
  e
  efancy '   help'
  efancy '   random'
  efancy '   assign'
  efancy '   complement'
  e
  erev 'If you want to show this intro-menu again, do:'
  e
  efancy '  show-intro'
  e
  erev 'You can also see more documentation at:'
  e
  e "  #{slateblue(URL_TO_THE_DOCUMENTATION)}"
  e
  erev 'If you feel that something is missing or incorrect, feel '\
       'free to send an email to:'
  e
  efancy "  #{EMAIL}"
  e
end

#show_t_phages ⇒ Object

#

show_t_phages

#


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# File 'lib/bioroebe/shell/shell.rb', line 2244

def show_t_phages
  dataset = YAML.load_file(
    ::Bioroebe.yaml_dir?+'viruses/ecoli_phages.yml'
  )
  # ======================================================================= #
  # Next, display that as a table.
  # ======================================================================= #
  erev 'Name of Phage | Plaque Size | Head diameter | tail length | latent period | burst size'
  cliner length: 88
  dataset.each_pair {|name_of_phage, value|
    print '|',name_of_phage.to_s.center(13),'|'
    # ===================================================================== #
    # Display the plague size next, aka small, medium or large.
    # ===================================================================== #
    plaque_size = value['plaque_size']
    print plaque_size.to_s.center(13),'|'
    head = value['head']
    print head.to_s.center(15),'|'
    tail = value['tail']
    print tail.to_s.center(13),'|'
    # ===================================================================== #
    # Display the latent period.
    # ===================================================================== #
    latent_period = value['latent_period']
    print latent_period.to_s.center(15),'|'
    burst_size = value['burst_size']
    print burst_size.to_s.center(12),'|'
    e
    cliner length: 88
  }
end

#show_taxid(id = 9606) ⇒ Object

#

show_taxid

This method will show the particular TaxID, using the NCBI taxonomy database.

The tax-id 9606 is “Homo sapiens”.

#


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# File 'lib/bioroebe/shell/shell.rb', line 1870

def show_taxid(
    id = 9606
  )
  id = 9606 if id.nil?
  id = id.to_s
  url = 'http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id='+id+'&lvl=0'
  erev 'The remote URL is: '+sfancy(url)
  webpage = open(url).read
  regex = /^<table width="100%"><tr><td valign="top"><h2>(Homo sapiens)<\/h2>/ # See: http://rubular.com/r/aQK5O8ZfGa
  webpage =~ regex
  name_of_the_organism = $1.to_s.dup
  erev 'The TaxID of '+simp(id)+rev+' corresponds to `'+
        sfancy(name_of_the_organism)+rev+'`.'
end

#show_the_aminoacids_frequencies ⇒ Object

#

show_the_aminoacids_frequencies

#


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# File 'lib/bioroebe/shell/shell.rb', line 7502

def show_the_aminoacids_frequencies
  pp YAML.load_file(FILE_AMINO_ACIDS_FREQUENCY)
end

#show_the_leader? ⇒ Boolean

#

show_the_leader?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6186

def show_the_leader?
  @internal_hash[:show_the_leader]
end

#show_the_positively_charged_aminoacids ⇒ Object

#

show_the_positively_charged_aminoacids

#


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# File 'lib/bioroebe/shell/shell.rb', line 768

def show_the_positively_charged_aminoacids
  result = <<-EOF
Lysine (K)
Arginine (R)
Histidine (H)
EOF
  e result
end

#show_the_trailer? ⇒ Boolean

#

show_the_trailer?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 6193

def show_the_trailer?
  @internal_hash[:show_the_trailer]
end

#show_the_weight_of_some_common_proteins(use_this_file = FILE_WEIGHT_OF_COMMON_PROTEINS) ⇒ Object

#

show_the_weight_of_some_common_proteins

#


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# File 'lib/bioroebe/shell/shell.rb', line 5175

def show_the_weight_of_some_common_proteins(
    use_this_file = FILE_WEIGHT_OF_COMMON_PROTEINS
  )
  erev 'Showing the weight of some common proteins next (in kDa):'
  e
  dataset = File.readlines(use_this_file).select {|line|
    line.include? ' # '
  }
  dataset.each {|line|
    splitted = line.split(':')
    key = splitted[0]
    value = splitted[1 .. -1].join(' ').strip
    erev "  #{(key+':').ljust(25)} "\
         "#{lightblue((value.to_s+' kDa').rjust(12))}"
  }
  e
end

#show_the_weight_of_the_four_individual_nucleotides ⇒ Object

#

show_the_weight_of_the_four_individual_nucleotides

#


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# File 'lib/bioroebe/shell/shell.rb', line 11145

def show_the_weight_of_the_four_individual_nucleotides
  e
  erev '  A: '+adenin?.rjust(10)+' '+
        palevioletred(weight_of_adenin?)
  erev '  T: '+thymin?.rjust(10)+' '+
        palevioletred(weight_of_thymin?)
  erev '  C: '+cytosin?.rjust(10)+' '+
        palevioletred(weight_of_cytosin?)
  erev '  G: '+guanin?.rjust(10)+' '+
        palevioletred(weight_of_guanin?)
  e
end

#show_this_sequence_padded(i = dna_sequence_object? ) ⇒ Object

#

show_this_sequence_padded

Usage example:

show_this_sequence_padded ATGACTTAGCCACAACTGCATGCATATGCATGACTGACT
#


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# File 'lib/bioroebe/shell/shell.rb', line 2356

def show_this_sequence_padded(
    i = dna_sequence_object?
  )
  if i.is_a? Array and i.empty?
    i << dna_sequence_object?
  end
  if i.is_a? Array
    i = i.join
  end
  # ======================================================================= #
  # First, split it into an array of 80 characters each.
  # ======================================================================= #
  array = i.scan(/.{,80}/).reject {|entry| entry.empty? }
  array.each {|entry|
    erev entry
  }
end

#show_this_subsequence(start_position = 1, end_position = 10, work_on_this_sequence = dna_sequence_object? ) ⇒ Object

#

show_this_subsequence

Sometimes we want to show a subsequence. This method helps us to do so, too.

The input may be “tainted”, e. g. be a String like “12,345” or “12.345”, so this method will have to eliminate the ‘,’ and ‘.’ characters as well, before converting this String into an Integer. (It must be an Integer because nucleotide counting can logically not be a Float.)

Usage example:

random 99; [22..33]
#


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# File 'lib/bioroebe/shell/shell.rb', line 1733

def show_this_subsequence(
    start_position        =  1,
    end_position          = 10,
    work_on_this_sequence = dna_sequence_object?
  )
  start_position = start_position.to_s.delete(',.').to_i
  end_position   = end_position.to_s.delete(',.').to_i
  if start_position < 1
    erev 'The minimum for the start-position must be 1, so this'
    erev 'is now treated as one rather than '+start_position.to_s+'.'
    start_position = 1
  end
  if end_position > work_on_this_sequence.size
    erev 'The sequence is '+slateblue('too long')+rev+' ('+
         crimson('end_position')+rev+' is '\
         'at '+sfancy(end_position.to_s)+rev+', '+
         nucleotides_or_aminoacids?.to_s+' sequence length '\
         'was: '+sfancy(work_on_this_sequence.size.to_s)+
         rev+').'
    erev 'It will be limited next to '+
         sfancy(work_on_this_sequence.size.to_s)+rev+' in length.'
    end_position = work_on_this_sequence.size
  end
  sequence = work_on_this_sequence.start_end(
    start_position,
    end_position
  )
  if sequence
    size = sequence.size.to_s
    nucleotides_or_aminoacids_or_empty = ''
    if work_on_this_sequence.respond_to? :nucleotides_or_aminoacids?
      nucleotides_or_aminoacids_or_empty = work_on_this_sequence.nucleotides_or_aminoacids?.to_s
    end
    erev 'Next showing a subsequence, '+
         nucleotides_or_aminoacids_or_empty+' '+
         olive(start_position.to_s)+rev+' to '+
         olive(end_position.to_s)+rev+
         ' (including '+olive(start_position.to_s)+
         rev+' and '+olive(end_position.to_s)+rev+').'
    erev 'The length of the fragment will be '+
         simp(size)+rev+' '+
         nucleotides_or_aminoacids_or_empty.strip+
         '.'
    report_this_dna_sequence_with_proper_trailer_and_leader(sequence) { :try_to_colourize_start_codon }
  else
    erev 'This subsequence appears to be invalid '\
         '(start: '+start_position.to_s+', end: '+end_position.to_s+')'
  end
end

#show_todo_file ⇒ Object

#

show_todo_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 5560

def show_todo_file
  cat '$RUBY_SRC/bioroebe/doc/TODO_FOR_THE_BIOROEBE_PROJECT.md'
end

#show_useful_URLs ⇒ Object

#

show_useful_URLs

This method will simply show some important, bioinformatics related URLs. In particular URLs that may be important for bioinformatics related tasks, e. g. NCBI, GeneBank and so forth.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2913

def show_useful_URLs
  result = <<-EOF

#{rev}NCBI:    #{sfancy(obtain_url_for(:ncbi))}
#{rev}GenBank: #{sfancy(obtain_url_for(:genbank))}
#{rev}PDB:     #{sfancy(obtain_url_for(:pdb))}
#{rev}Prosite: #{sfancy(obtain_url_for(:prosite))}

EOF
  e result
end

#show_weight_of_this_nucleotide(i) ⇒ Object

#

show_weight_of_this_nucleotide

Use this method to show the total weight of a specific nucleotide.

Usage examples:

weight? U
weight? T
weight? Adenine
#


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# File 'lib/bioroebe/shell/shell.rb', line 5529

def show_weight_of_this_nucleotide(i)
  i = i.to_s
  if i.empty?
    erev 'Please supply a nucleotide, such as "Adenine" or "A".'
    erev 'Note that the short variant is preferred.'
    return
  end
  i = i[0,1] if i.size > 1
  _ = FILE_NUCLEOTIDES_WEIGHT # bl /Users/x/DATA/SCIENCE/YAML/nucleotides_weight.yml
  if File.exist?(_)
    _ = YAML.load_file(_)
    dataset = {}
    _.each_pair {|key, value|
      dataset[key[0,1]] = value
    }
    if dataset.has_key?(i)
      erev 'The weight of '+sfancy(i)+rev+' is: '+
        sfancy(
          ChemistryParadise.atomic_mass_of(dataset[i])
        )
    else
      erev 'The key `'+sfancy(i)+rev+'` was not found.'
    end
  else
    ewarn 'We did not find a required file at '+sfile(_)+rev+'.'
  end
end

#show_welcome_message ⇒ Object

#

show_welcome_message

Show a little welcome message on startup. This can be disabled of course.

#


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# File 'lib/bioroebe/shell/shell.rb', line 8241

def show_welcome_message
  unless silent_startup?
    erev 'Welcome to the '+violet('Bioroebe::Shell')+
         rev+' Version '+
         sfancy(version?.to_s)+
         rev+
         ', last updated: '+
         simp(::Bioroebe.last_updated?)+
         rev+'.'
    erev "Type \"#{sfancy('help')}#{rev}\" to get some help."
  end
end

#show_xorg_buffer ⇒ Object

#

show_xorg_buffer

#


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# File 'lib/bioroebe/shell/shell.rb', line 3051

def show_xorg_buffer
  if @internal_hash[:use_xsel]
    esystem 'xsel -o'
  end
end

#showorf(i = dna_sequence_object?, , show_how_many_frames = :show_three_frames) ⇒ Object

#

showorf (showorf tag)

Use this method to show the open reading frame of a given sequence.

We can also use it to selectively show a certain frame, such as frame2. See class Bioroebe::ShowOrf for this.

Note that in May 2020 (10.05.2020) class Bioroebe::ShowOrf here was replaced with

#


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# File 'lib/bioroebe/shell/shell.rb', line 5929

def showorf(
    i                    = dna_sequence_object?,
    show_how_many_frames = :show_three_frames
  )
  i = dna_sequence_object? if i.nil?
  i = dna_sequence_object? if i.is_a?(Array) and i.empty?
  display_open_reading_frames(i) { show_how_many_frames }
end

#shuffle_main_string ⇒ Object

#

shuffle_main_string

This method will re-arrange the main DNA sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10028

def shuffle_main_string
  erev 'Shuffling the main DNA string next.'
  _ = dna_sequence?.split(//).shuffle.join
  set_dna_string(_, :be_quiet)
  show_dna_sequence
end

#silent_startup? ⇒ Boolean

#

silent_startup?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8068

def silent_startup?
  @internal_hash and @internal_hash[:silent_startup]
end

#start_clipboard(i = '"') ⇒ Object

#

start_clipboard

Make use of the clipboard here.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7186

def start_clipboard(i = '"')
  _ = @internal_hash[:clipboard]
  if _
    erev 'Starting Clipboard now (exit it with '+i+')'
    _.set_exit_token(i) # Set closing token. Default to }
    _.fetch_input
    return _.buffer?
  end
end

#start_codon? ⇒ Boolean

#

start_codon?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 2221

def start_codon?
  ::Bioroebe.start_codon?
end

#start_gtk_controller ⇒ Object

#

start_gtk_controller

#


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# File 'lib/bioroebe/shell/shell.rb', line 8497

def start_gtk_controller
  require 'bioroebe/gui/gtk3/controller/controller.rb'
  ::Bioroebe.run_gtk_controller
end

#start_search(be_verbose = true) ⇒ Object

#

start_search (start_search tag)

This will attempt to locate @search_for substring in the main nucleotide sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 7941

def start_search(
    be_verbose = true
  )
  case be_verbose
  when :be_quiet
    be_verbose = false
  end
  _ = search_for? # Obtain a handle to the sequence we are trying to find.
  if _
    results = sequence?.scan(_)
    if be_verbose
      erev "Trying to now find `#{simp(_)}#{rev}`."
      pp results
    end
    msg = "We found `#{simp(results.size.to_s)}#{rev}` entr".dup
    if (results.size > 1) or (results.size == 0)
      msg << 'ies' # Plural form.
    else
      msg << 'y'   # Singular form.
    end
    msg << '.'
    erev msg
    return results.size
  else
    erev "No value for #{paleturquoise('@search_for')}#{rev} was "\
         "set yet. Please set one via invoking:"
    e
    erev '  set_search_for'
    e
  end
end

#stop_codons? ⇒ Boolean

#

stop_codons?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 2228

def stop_codons?
  ::Bioroebe.stop_codons?
end

#store_here? ⇒ Boolean

#

store_here?

Where to store output generated by BioRoebe. Should point to a locally existing directory.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 3841

def store_here?
  ::Bioroebe.store_here?
end

#three_to_one(i) ⇒ Object

#

three_to_one

This method will translate, and output, a three-letter aminoacid into the corresponding single-letter code.

Invocation example:

three_to_one Thr Thr Glu Ala Val Glu Ser Thr Val Ala Thr Leu Glu Asp Ser # => T T E A V E S T V A T L E D S
3to1 ARG-ALA-SER-LEU-PHE-TRP-LYS-HIS-ASN-SER-VAL-LEU-ILE-VAL-PRO
#


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# File 'lib/bioroebe/shell/shell.rb', line 2304

def three_to_one(i)
  if i.is_a? Array
    i = i.join('-').strip
  end
  e ::Bioroebe.three_to_one(i).strip
end

#thymin? ⇒ Boolean

#

thymin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8332

def thymin?
  YAML.load_file(FILE_NUCLEOTIDES)['Thymin']
end

#tk_start_three_to_one ⇒ Object

#

start_three_to_one

Mostly an ad-hoc way to load up a specific ruby-tk widget.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6611

def tk_start_three_to_one
  require 'bioroebe/gui/tk/three_to_one/three_to_one.rb'
  Bioroebe::GUI::Tk::ThreeToOne.new(ARGV)
end

#to_dna(i = sequence? ) ⇒ Object

#

to_dna

#


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# File 'lib/bioroebe/shell/shell.rb', line 9215

def to_dna(
    i = sequence?
  )
  if i.nil?
    if seq?
      i = seq?
    elsif aminoacids? # Handle Aminoacids here.
      i = aminoacids?
      return
    end
  end
  erev padding?+
       dna_with_ends(Bioroebe.to_dna(i))
end

#to_fasta(i = dna_sequence? ) ⇒ Object

#

to_fasta

Create a Fasta format from the target sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3701

def to_fasta(
    i = dna_sequence?
  )
  array = i.scan(/.{,80}/).reject {|entry| entry.empty? }
  name_of_the_gene = sequence_object?.name_of_gene?.to_s
  if name_of_the_gene.empty?
    name_of_the_gene << 'Drosophila melanogaster chromosome'
  end
  array[0,0] = '>gi|671162122:c7086083-7083225 '+name_of_the_gene
  e array.join(N)
end

#to_genbank(this_sequence = dna_sequence_as_string? ) ⇒ Object

#

to_genbank

This method will generate, or rather output, the GenBank file format.

#


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# File 'lib/bioroebe/shell/shell.rb', line 4934

def to_genbank(
    this_sequence = dna_sequence_as_string?
  )
  if fasta?
    id = fasta?.sequence_id?
    # ===================================================================== #
    # bl $BIOROEBE/genbank/genbank_flat_file_format_generator.rb
    # ===================================================================== #
    _ = GenbankFlatFileFormatGenerator.new(this_sequence, :do_not_run_yet)
    _.use_this_as_id = id
    _.run
  elsif !this_sequence.empty?
    GenbankFlatFileFormatGenerator.new(this_sequence)
  else
    erev 'There does not seem to be any FASTA sequence assigned.'
  end
end

#to_rna(i = seq_object?) ) ⇒ Object

#

to_rna

#


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# File 'lib/bioroebe/shell/shell.rb', line 11088

def to_rna(i = seq_object?)
  i = seq_object? if i.nil? # Assign to default in this case.
  if i.respond_to? :to_rna
    i = i.to_rna
  end
  erev i
end

#to_talen(i = dna_sequence? ) ⇒ Object

#

to_talen

#


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# File 'lib/bioroebe/shell/shell.rb', line 10808

def to_talen(
    i = dna_sequence?
  )
  i = dna_sequence? if i.nil? # Obtain the DNA sequence.
  talen_sequence = '' # This will contain our final talen-sequence.
  talens = YAML.load_file(::Bioroebe.file_talens)
  i.scan(/./).each {|char|
    talen_sequence << "{ #{talens[char]} }"
  }
  pp talen_sequence
end

#toggle_mode ⇒ Object

#

toggle_mode

#


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# File 'lib/bioroebe/shell/shell.rb', line 4325

def toggle_mode
  case @internal_hash[:mode]
  when :dna
    set_mode(:aminoacid)
  else
    set_mode(:dna)
  end
end

#toggle_truncate ⇒ Object

#

toggle_truncate

#


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# File 'lib/bioroebe/shell/shell.rb', line 9321

def toggle_truncate
  if do_truncate?
    do_not_truncate
  else
    ::Bioroebe.do_truncate
    erev 'We will truncate too-long output.'
  end
end

#toggle_xorg_buffer ⇒ Object

#

toggle_xorg_buffer

#


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# File 'lib/bioroebe/shell/shell.rb', line 8693

def toggle_xorg_buffer
  @configuration.additionally_set_xorg_buffer = !@configuration.additionally_set_xorg_buffer
  @configuration.save
end

#trailing_3_prime(get_rid_of_spaces = false) ⇒ Object Also known as: three_trailer, three_trailer?, trailer, three_prime, trailing_three_prime, trail_three_prime, trail_three, trailing_three

#

trailing_3_prime

This will essentually return a “ -3’” string.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6078

def trailing_3_prime(
    get_rid_of_spaces = false
  )
  if show_the_trailer?
    get_rid_of_spaces = true if get_rid_of_spaces == :no_spaces
    _ = " - 3'".dup
    _.delete!(' ') if get_rid_of_spaces
    return _
  end
  return '' # Else return an empty String.
end

#trailing_five_prime ⇒ Object Also known as: trailing_5_prime, five_prime_trailer

#

trailing_five_prime

#


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# File 'lib/bioroebe/shell/shell.rb', line 6724

def trailing_five_prime
  " - 5'"
end

#translate(i, be_verbose = true) ⇒ Object

#

translate

General translate method.

#


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# File 'lib/bioroebe/shell/shell.rb', line 3139

def translate(i, be_verbose = true)  # Translate tag.
  translate_aminoacid(i, be_verbose) # for now, we default to this.
end

#translate_aminoacid(these_aminoacids = string?, , be_verbose = true) ⇒ Object

#

translate_aminoacid

Translate aminoacids from one letter to full name.

Usage example:

translate kkrnn
#


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# File 'lib/bioroebe/shell/shell.rb', line 7034

def translate_aminoacid(
    these_aminoacids = string?,
    be_verbose       = true
  )
  these_aminoacids = string? if these_aminoacids.nil?
  if these_aminoacids.include? ','
    these_aminoacids.delete!(',')
  end
  if these_aminoacids == '?'
    erev 'Help requested:' # The user requested help here.
    erev '  '+sfancy('-> ')+rev+'Simply input some AminoAcids here.'
    erev '  '+sfancy('-> ')+rev+'for instance, "translate kkrrr".'
  else
    if these_aminoacids
      these_aminoacids = these_aminoacids.join(' ') if these_aminoacids.is_a? Array
      these_aminoacids.gsub!(/#{N}/,'')
      _ = these_aminoacids.gsub(/ /,'').upcase
      if be_verbose
        erev 'Now translating one letter Aminoacid to '\
             'their full names: '
        print '    '+these_aminoacids.upcase
      end
      _ = ::Bioroebe.translate(_)
      if use_colours?
        _ = sienna(_) if Object.const_defined? :Colours
      end
      erev ' -> '+_ # Invoke .translate if be_verbose
      return _
    end
  end
end

#translate_dna_into_aminoacid(i = dna_sequence?, , frame = 1) ⇒ Object Also known as: translate_dna_into_aminoacid_frame1

#

translate_dna_into_aminoacid

The first argument should be the DNA sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 908

def translate_dna_into_aminoacid(
    i     = dna_sequence?,
    frame = 1
  )
  i = dna_sequence? if i.nil?
  if i.is_a? Array
    i.each {|entry| translate_dna_into_aminoacid(entry) }
  else
    i.upcase!
    case frame
    when 1 # normal frame, default.
    when 2 # one shifted
      i[0,1] = ''
    when 3 # two shifted
      i[0,1] = ''
      i[0,1] = ''
    end
    # ===================================================================== #
    # Next, return the result.
    # ===================================================================== #
    return ::Bioroebe.translate_dna_into_aminoacid(i)
  end
end

#translate_dna_into_aminoacid_frame2(i = nil) ⇒ Object

#

translate_dna_into_aminoacid_frame2

#


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# File 'lib/bioroebe/shell/shell.rb', line 891

def translate_dna_into_aminoacid_frame2(i = nil)
  translate_dna_into_aminoacid(i, 2) # Frame 2.
end

#translate_dna_into_aminoacid_frame3(i = nil) ⇒ Object

#

translate_dna_into_aminoacid_frame3

#


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# File 'lib/bioroebe/shell/shell.rb', line 898

def translate_dna_into_aminoacid_frame3(i = nil)
  translate_dna_into_aminoacid(i, 3) # Frame 3.
end

#try_to_compare_these_two_sequences_for_equality(i) ⇒ Object

#

try_to_compare_these_two_sequences_for_equality

This method will compare two sequences for equality, e. g. will return true or false, depending on whether they are equal or not.

nil will be returned if the method could not find the necessary ‘==’ characters.

Invocation example from within a running bio-shell:

ATCGATCGATCG == ATCGATCG
#


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# File 'lib/bioroebe/shell/shell.rb', line 9979

def try_to_compare_these_two_sequences_for_equality(i)
  i.strip!
  if i.include? '=='
    splitted = i.split('==').map(&:strip)
    # ===================================================================== #
    # Do the comparison next.
    # ===================================================================== #
    splitted.first == splitted.last
  else
    nil
  end
end

#try_to_display_this_fasta_entry(i) ⇒ Object

#

try_to_display_this_fasta_entry

#


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# File 'lib/bioroebe/shell/shell.rb', line 8843

def try_to_display_this_fasta_entry(i)
  if i.is_a? String
    i = i.to_i - 1 # -1 because Arrays in ruby begin at 0.
  end
  last_entry = array_fasta?.last
  sequence_data = last_entry[i]
  erev sequence_data
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :and_assign_it_as_well
    # ===================================================================== #
    when :and_assign_it_as_well
      assign(sequence_data) # In this case it will become the new main sequence data.
    end
  end
end

#try_to_find_restriction_enzymes_for(i) ⇒ Object Also known as: find_this_sequence, find_in_main_sequence

#

try_to_find_restriction_enzymes_for

This method name is a slight misnomer; we can simply find any target sequence.

The method can also handle some Symbols as input, such as the symbol :shine_dalgarno, which will be replaced accordingly to the SD sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6365

def try_to_find_restriction_enzymes_for(
    i
  )
  # ======================================================================= #
  # === We always have to work with an Array as input
  # ======================================================================= #
  unless i.is_a? Array
    i = [i]
  end
  i.map! {|entry|
    case entry # Use special sequences.
    when :shine_dalgarno
      entry = 'AGGAGGT'
    end
    # ===================================================================== #
    # Past this point, we will assume a String as input. But we will have
    # to make sure, still.
    # ===================================================================== #
    entry = entry.to_s unless entry.is_a? String
    entry.delete!('-') if entry.include? '-'
    entry
  }
  i.each {|entry|
    report_main_sequence(entry) { :with_ruler }
    possible_results = dna_string?.scan(/#{entry}/)
    unless possible_results.empty?
      e
      erev "Start nucleotide position is at: "\
           "#{simp((dna_string?.index(entry)+1))}#{rev}"
      e
    end
  }
end

#try_to_find_this_restriction_enzyme(i) ⇒ Object

#

try_to_find_this_restriction_enzyme

Use this method to find a specific restriction enzyme.

The restriction enzymes are stored in this yaml file here:

bl $BIOROEBE/yaml/restriction_enzymes/restriction_enzymes.yml

Usage example:

MvnI?
#


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# File 'lib/bioroebe/shell/shell.rb', line 9102

def try_to_find_this_restriction_enzyme(i)
  i = i.dup if i.frozen?
  i.delete!('?') # We do not need any '?' characters.
  original_input = i.dup
  # i = i.downcase # No longer downcase since as of June 2018.
  if i.include? 'restriction'
    i.sub!(/restriction/,'')
  end
  if i.include? '.site' # Assume a syntax such as: Restriction.EcoRI.site
    e ::Bioroebe.restriction_enzyme(i)
  else # else it will be more verbose
    i.delete!('.') if i.include? '.'
    if i.end_with?('1') and !::Bioroebe.has_this_restriction_enzyme?(i) # Is invalid. 
      erev 'The input `'+simp(i)+rev+'` ends with the number 1. This '\
           'is not possible, so'
      erev 'we replace the trailing 1 with a capital I.'
      i[-1,1] = 'i' # Ok not a capital one, because we store in a downcased variant.
      original_input[-1,1] = 'I'
    end
    if ::Bioroebe.has_this_restriction_enzyme? i
      target_sequence_data = ::Bioroebe.return_restriction_enzyme_sequence_and_cut_position(i)
      # =================================================================== #
      # Tap into the method Bioroebe.restriction_enzyme
      # =================================================================== #
      _ = ::Bioroebe.restriction_enzyme(i) # bl $BIOROEBE/module_methods.rb
      erev "We have found a restriction enzyme called "\
           "#{sfancy(original_input)}#{rev}."
      e
      e "#{rev}The sequence this #{mediumorchid(_.size.to_s+'-cutter')}#{rev}"\
        " relates to is: `"\
        "#{sfancy(five_prime+simp(_)+rev)}"\
        "#{sfancy(three_trailer)}#{rev}`"
      e
      # =================================================================== #
      # The variable target_sequence_data will look like this:
      #   ["GCCNNNNNGGC", "7", "7"]
      # =================================================================== #
      if target_sequence_data.last == :blunt
        erev "This restriction enzyme will produce a "\
             "#{seagreen('blunt')}#{rev} overhang."
        e
      else
        erev "This restriction enzyme will produce a "\
             "#{seagreen('sticky-end')}#{rev} overhang."
        e
      end
      # =================================================================== #
      # Next, show the exact cut that will be made.
      # =================================================================== #
      sequence = ::Bioroebe.return_sequence_that_is_cut_via_restriction_enzyme(i)
      erev 'It will specifically cut between:     '+
            sfancy(five_prime)+rev+
            simp(sequence)+
            sfancy(three_trailer)+rev
      # =================================================================== #
      # And the complementary sequence follows next. The colour used
      # is swarn().
      # =================================================================== #
      complementary_sequence = reverse(
        Colours.remove_escape_sequences(sequence)
      )
      # =================================================================== #
      # We must insert a | at the right position.
      # =================================================================== #
      target_sequence_data = target_sequence_data[1].to_i
      complementary_sequence[-target_sequence_data,0] = swarn('|')+rev
      erev ''.ljust(38)+sfancy(leading_three_prime)+rev+
           complementary_sequence+rev+
           sfancy(five_prime_trailer)+rev
    else
      erev 'We were unable to find a restriction enzyme called '\
           '`'+sfancy(i)+'`'+rev
    end
  end
end

#try_to_report_the_version_of_bedtools ⇒ Object

#

try_to_report_the_version_of_bedtools

#


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# File 'lib/bioroebe/shell/shell.rb', line 9665

def try_to_report_the_version_of_bedtools
  result = `bedtools --version 2>&1`
  if result.include? 'command not found'
    e
    erev 'The bedtools do not appear to be installed / available.'
    e
    if is_on_roebe?
      erev 'You may be able to install it via:'
      e
      erev '  rbt bedtools'
      e
    end
  else
    version = result.sub(/bedtools/,'').strip.to_s.delete('v')
    erev "The version of bedtools is: "\
         "#{orange(version)}#{rev}"
  end
end

#try_to_report_the_version_of_viennarna ⇒ Object

#

try_to_report_the_version_of_viennarna

This method can be used to see the version of ViennaRNA, if it is installed at all.

#


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# File 'lib/bioroebe/shell/shell.rb', line 6336

def try_to_report_the_version_of_viennarna
  result = `RNAplfold --version 2>&1`
  if result.include? 'command not found'
    e
    erev 'ViennaRNA does not appear to be installed / available.'
    e
    if is_on_roebe?
      erev 'You may be able to install it via:'
      e
      erev '  rbt viennarna'
      e
    end
  else
    version = result.sub(/RNAplfold/,'').strip.to_s
    erev 'The version of ViennaRNA is: '+
       orange(version)+rev
  end
end

#try_to_run_rnalfold_on_this_file(i) ⇒ Object

#

try_to_run_rnalfold_on_this_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 7527

def try_to_run_rnalfold_on_this_file(i)
  if File.exist? i
    esystem("RNALfold --infile=#{i}")
  else
    erev 'No file called `'+sfile(i)+rev+'` exists.'
  end
end

#try_to_show_the_configuration ⇒ Object

#

try_to_show_the_configuration

#


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# File 'lib/bioroebe/shell/shell.rb', line 2968

def try_to_show_the_configuration
  @configuration.show_config if @configuration.respond_to? :show_config
  _ = verbose_truth(use_expand_cd_aliases?)
  colourized_yes_or_no = simp(_.to_s)
  erev 'Will we use class Rcfiles::DirectoryAliases: '+
       colourized_yes_or_no
end

#type? ⇒ Boolean

#

type?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 4811

def type?
  sequence?.type?
end

#uncolourize_this_aminoacid(i) ⇒ Object

#

uncolourize_this_aminoacid

#


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# File 'lib/bioroebe/shell/shell.rb', line 10915

def uncolourize_this_aminoacid(i)
  if i.nil?
    erev 'Please supply an argument, an aminoacid. Either one '\
         'letter or the full name.'
    return
  end
  unless ::Bioroebe.array_colourize_this_aminoacid.include? i
    erev 'We will no longer colourize the '\
         'aminoacid `'+swarn(i)+'`.'
    ::Bioroebe.array_colourize_this_aminoacid.delete i # Using .delete() works here.
  end
end

#unfreeze_the_main_sequence ⇒ Object

#

unfreeze_the_main_sequence

#


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# File 'lib/bioroebe/shell/shell.rb', line 5366

def unfreeze_the_main_sequence
  @internal_hash[:the_main_sequence_is_frozen] = false
end

#uniprot_fetch(i = 'P12345') ⇒ Object

#

uniprot_fetch

This method can be sued to obtain the .fasta sequence of a protein listed at uniprot.

#


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# File 'lib/bioroebe/shell/shell.rb', line 720

def uniprot_fetch(
    i = 'P12345'
  )
  i = 'P12345' if i.nil?
  return ::Bioroebe.fetch_data_from_uniprot(i).string?
end

#upcase_main_string ⇒ Object

#

upcase_main_string

Use this method to upcase the main sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 11163

def upcase_main_string
  set_sequence(sequence?.upcase)
end

#uracil? ⇒ Boolean

#

uracil?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8325

def uracil?
  YAML.load_file(FILE_NUCLEOTIDES)['Uracil']
end

#use_expand_cd_aliases? ⇒ Boolean

#

use_expand_cd_aliases?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 5668

def use_expand_cd_aliases?
  ::Bioroebe::Configuration.use_expand_cd_aliases?
end

#use_this_fasta_file(at_position = 1) ⇒ Object

#

use_this_fasta_file

Use a fasta file based on its position.

For instance, fasta file at position 2 will be the second fasta file kept in the main log directory.

#


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# File 'lib/bioroebe/shell/shell.rb', line 2202

def use_this_fasta_file(
    at_position = 1
  )
  # ======================================================================= #
  # We need to map the given position to the existing (local) file at hand.
  # ======================================================================= #
  this_fasta_file = return_fasta_files_in_the_log_directory[at_position.to_i - 1]
  if this_fasta_file
    assign_fasta(this_fasta_file)
  else
    erev 'Could not find any file at position '+simp(at_position.to_s)+rev+'.'
    erev 'Use "'+steelblue('show_fasta_files')+rev+
         '" to see which fasta files are available.'
  end
end

#use_which_prompt? ⇒ Boolean

#

use_which_prompt?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8094

def use_which_prompt?
  @internal_hash[:prompt_to_use]
end

#use_xsel? ⇒ Boolean

#

use_xsel?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 7269

def use_xsel?
  @internal_hash[:use_xsel]
end

#user_input? ⇒ Boolean

#

user_input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 11757

def user_input?
  @internal_hash[:user_input]
end

#verbose_handle_this_sys_command(i, arguments = a? ) ⇒ Object

#

verbose_handle_this_sys_command

#


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# File 'lib/bioroebe/shell/shell.rb', line 4198

def verbose_handle_this_sys_command(
    i, arguments = a?
  )
  if a and a.is_a?(Array)
    arguments = a.join(' ').strip
  end
  esystem i+' '+arguments.to_s+' &'
end

#verbose_report_numbered_amino_acid_sequence(i, which_frame = '1') ⇒ Object

#

verbose_report_numbered_amino_acid_sequence

This method can be used to show a verbose and properly-aligned frame shift table for the given aminoacid sequence.

#


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# File 'lib/bioroebe/shell/shell.rb', line 10877

def verbose_report_numbered_amino_acid_sequence(
    i,
    which_frame = '1'
  )
  n_chunks = ::Bioroebe::Configuration.n_chunks?
  erev 'The amino acid sequence, with numbers and split into chunks '\
       'of '+plum(n_chunks.to_s)+rev+', for '+
       sfancy('Frame '+which_frame.to_s)+rev+' is: '
  e # Newline is good.
  chars = i.chars
  # ======================================================================= #
  # Split into lines of 40, or rather what value was given to n_chunks.
  # ======================================================================= #
  slice = chars.each_slice(n_chunks).to_a
  position = 1
  slice.each {|array|
    print '  '
    array.each {|char|
      char = char.rjust(3)
      char = ::Bioroebe.colourize_aa(char)
      print rev+char+rev+swarn('|')+rev
    }; e # Do a newline for good measure.
    print '  ' # Always have two ' ' before a new line.
    # ===================================================================== #
    # === Show the position of the aminoacid next
    # ===================================================================== #
    array.size.times {
      print forestgreen(position.to_s.rjust(3))+rev+swarn('|')+rev
      position += 1
    }
    e; e
  }
  e
end

#verbose_save_history_to_file ⇒ Object

#

verbose_save_history_to_file

#


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# File 'lib/bioroebe/shell/shell.rb', line 8156

def verbose_save_history_to_file
  erev 'We will next save the input-history into a file.'
  save_history_to_file
end

#version? ⇒ Boolean

#

version?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 8061

def version?
  ::Bioroebe.version
end

#weight_of_adenin? ⇒ Boolean

#

weight_of_adenin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 2599

def weight_of_adenin?
  ChemistryParadise::CalculateAtomicMass[adenin?].to_s.ljust(7,'0')
end

#weight_of_cytosin? ⇒ Boolean

#

weight_of_cytosin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 2613

def weight_of_cytosin?
  ChemistryParadise::CalculateAtomicMass[cytosin?].to_s.ljust(7,'0')
end

#weight_of_guanin? ⇒ Boolean

#

weight_of_guanin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 2627

def weight_of_guanin?
  ChemistryParadise::CalculateAtomicMass[guanin?].to_s.ljust(7,'0')
end

#weight_of_thymin? ⇒ Boolean

#

weight_of_thymin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 2606

def weight_of_thymin?
  ChemistryParadise::CalculateAtomicMass[thymin?].to_s.ljust(7,'0')
end

#weight_of_uracil? ⇒ Boolean

#

weight_of_uracil?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 2620

def weight_of_uracil?
  ChemistryParadise::CalculateAtomicMass[uracil?].to_s.ljust(7,'0')
end

#wget(i) ⇒ Object

#

wget (wget tag)

Simply use wget to download remote files.

#


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# File 'lib/bioroebe/shell/shell.rb', line 5087

def wget(i)
  if i.is_a? Array
    i.each {|entry| wget(entry) }
  else
    unless i.start_with? 'wget '
      i = "wget #{i}"
    end
    esystem i
  end
end

#what_sequence_is_this?(i = dna_sequence? ) ⇒ Boolean

#

what_sequence_is_this?

This method attempts to find common sequences.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 1631

def what_sequence_is_this?(
    i = dna_sequence?
  )
  erev 'The sequence length is '+i.size.to_s+'.'
  # ======================================================================= #
  # Obtain the corresponding aminoacid sequence next.
  # ======================================================================= #
  aa_sequence = ::Bioroebe.dna_to_aa(i)
  if aa_sequence.include? ::Bioroebe.ubiquitin
    erev 'The aminoacid sequence has at least one Ubiquitin-related sequence.'
  end
end

#will_we_truncate? ⇒ Boolean

#

will_we_truncate?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 9340

def will_we_truncate?
  if do_truncate?
    erev 'We will truncate.'
  else
    erev 'We will not truncate.'
  end
end

#will_we_use_colours? ⇒ Boolean

#

will_we_use_colours?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/shell/shell.rb', line 4210

def will_we_use_colours?
  erev "Will we use colours? #{verbose_truth(@use_colours)}#{rev}"
end

#www_finder_run ⇒ Object

#

www_finder_run

#


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# File 'lib/bioroebe/shell/shell.rb', line 3772

def www_finder_run
  Bioroebe::GUI::Gtk::WwwFinder.run
end