Class: Bioroebe::Shell
- Inherits:
-
CommandlineApplication
- Object
- Base
- CommandlineApplication
- Bioroebe::Shell
- 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
Class Method Summary collapse
-
.[](i = ARGV) ⇒ Object
# === Bioroebe::Shell[] ========================================================================= #.
-
.colour? ⇒ Boolean
# === Bioroebe::Shell.colour?.
-
.generate_pdf_tutorial(also_upload_the_tutorial = true) ⇒ Object
# === Bioroebe::Shell.generate_pdf_tutorial.
-
.menu(i = ARGV) ⇒ Object
# === Bioroebe::Shell.menu.
-
.return_entries_in_the_current_directory ⇒ Object
# === Bioroebe::Shell.return_entries_in_the_current_directory ========================================================================= #.
-
.set_colour(i) ⇒ Object
# === Bioroebe::Shell.set_colour.
-
.upload_this_pdf_file(path) ⇒ Object
# === Bioroebe::Shell.upload_this_pdf_file.
Instance Method Summary collapse
-
#aa_to_dna(i) ⇒ Object
# === aa_to_dna ========================================================================= #.
-
#add_his_tag(i = 'add 6 random his tags') ⇒ Object
# === add_his_tag.
-
#add_n_nucleotides ⇒ Object
# === add_to_start.
-
#add_poly_a_sequence ⇒ Object
# === add_poly_a_sequence.
-
#add_the_current_user_input_to_the_history ⇒ Object
# === add_the_current_user_input_to_the_history ========================================================================= #.
-
#add_timer_snapshot ⇒ Object
# === add_timer_snapshot ========================================================================= #.
-
#add_to_end(i) ⇒ Object
(also: #add)
# === add_to_end.
-
#add_to_history(i = user_input? ) ⇒ Object
(also: #append_this_onto_the_history)
# === add_to_history.
-
#add_to_start(i) ⇒ Object
(also: #left_add)
# === add_to_start ========================================================================= #.
-
#add_to_start_or_end(i = '', append_or_prepend = :append) ⇒ Object
# === add_to_start_or_end.
-
#add_vertical_barrier_to_sequence(i = dna_sequence? ) ⇒ Object
# === add_vertical_barrier_to_sequence.
-
#adenin? ⇒ Boolean
# === adenin?.
-
#align_ORFS(i = dna_string? ) ⇒ Object
# === align_ORFS.
-
#all_arguments? ⇒ Boolean
(also: #a?)
# === all_arguments? (a? tag) ========================================================================= #.
-
#all_upcase?(i) ⇒ Boolean
(also: #is_all_upcase?)
# === all_upcase?.
-
#analyze(i = sequence? ) ⇒ Object
# === analyze (analyze tag).
-
#analyze_dna_string(i = dna_string? ) ⇒ Object
# === analyze_dna_string.
-
#annotate_this_file(i) ⇒ Object
# === annotate_this_file ========================================================================= #.
-
#append(i) ⇒ Object
# === append (append tag).
-
#array_fasta? ⇒ Boolean
# === array_fasta? ========================================================================= #.
-
#array_history? ⇒ Boolean
# === array_history?.
-
#array_timer_snapshots? ⇒ Boolean
# === array_timer_snapshots? ========================================================================= #.
-
#assign_sequence2(i) ⇒ Object
# === assign_sequence2 ========================================================================= #.
-
#assume_what_type_this_is(i) ⇒ Object
# === assume_what_type_this_is.
-
#attempt_to_discover_dna_A_boxes ⇒ Object
# === attempt_to_discover_dna_A_boxes ========================================================================= #.
-
#automatically_rename_this_fasta_file(i) ⇒ Object
# === automatically_rename_this_fasta_file ========================================================================= #.
-
#backtranseq(i = aminoacid_sequence?, , output_as_dna_or_rna = :dna) ⇒ Object
(also: #translate_aminoacids_into_dna)
# === backtranseq.
-
#bioshell_log_dir? ⇒ Boolean
# === bioshell_log_dir?.
-
#bisulfite(i) ⇒ Object
# === bisulfite ========================================================================= #.
-
#calculate_atp_cost_for(i = aminoacid_sequence?) ) ⇒ Object
# === calculate_atp_cost_for.
-
#calculate_exponential_growth(a, b) ⇒ Object
# === calculate_exponential_growth ========================================================================= #.
-
#calculate_hamming_distance_of(i) ⇒ Object
# === calculate_hamming_distance_of.
-
#calculate_melting_temperature(i) ⇒ Object
# === calculate_melting_temperature.
-
#calculate_time_difference ⇒ Object
# === calculate_time_difference ========================================================================= #.
-
#calculcate_at_content(i = dna_sequence? ) ⇒ Object
# === calculcate_at_content.
-
#calculcate_gc_content(i = dna_sequence_as_string? ) ⇒ Object
# === calculcate_gc_content.
-
#change_first_nucleotide_to(i = dna_sequence? ) ⇒ Object
# === change_first_nucleotide_to.
-
#chdir(i = :default) ⇒ Object
(also: #cd)
# === chdir (cd tag) ========================================================================= #.
-
#check_for_local_vectors ⇒ Object
# === check_for_local_vectors ========================================================================= #.
-
#check_for_mismatches ⇒ Object
# === check_for_mismatches ========================================================================= #.
-
#chop(i = 1, chop_from_left_or_right_hand_side = :default) ⇒ Object
(also: #remove_n_nucleotides)
# === chop (chop tag).
-
#chop_to(i) ⇒ Object
# === chop_to.
-
#chunked_display(i = dna_sequence? ) ⇒ Object
# === chunked_display.
-
#clear(i) ⇒ Object
# === clear.
-
#coding_area? ⇒ Boolean
# === coding_area?.
-
#codon(i = sequence? ) ⇒ Object
(also: #codons, #codon?, #codons?)
# === codon.
-
#codon_to_aminoacid(i) ⇒ Object
# === codon_to_aminoacid.
-
#colour_for_nucleotide(i = '') ⇒ Object
(also: #colour_for_nucleotides)
# === colour_for_nucleotide ========================================================================= #.
-
#colour_for_stop_codon(i) ⇒ Object
# === colour_for_stop_codon ========================================================================= #.
-
#colour_scheme_demo(use_this_sequence = 'ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC') ⇒ Object
# === colour_scheme_demo ========================================================================= #.
-
#colour_scheme_for_aminoacids(i = aminoacid_sequence? ) ⇒ Object
# === colour_scheme_for_aminoacids.
-
#colour_scheme_for_nucleotides(i = dna_sequence? ) ⇒ Object
# === colour_scheme_for_nucleotides.
-
#colourize_fasta_file(i) ⇒ Object
# === colourize_fasta_file.
-
#colourize_nucleotide(i, add_leading_five_and_trailing_three_primes = true) ⇒ Object
(also: #colourize_nucleotide_sequence)
# === colourize_nucleotide.
-
#colourize_this_aminoacid(i) ⇒ Object
# === colourize_this_aminoacid.
-
#command_to_be_passed_to_the_menu? ⇒ Boolean
# === command_to_be_passed_to_the_menu? ========================================================================= #.
-
#compact_file(this_file = nil) ⇒ Object
# === compact_file.
-
#compare_two_files(file_a, file_b) ⇒ Object
# === compare_two_files.
-
#compare_two_strings_as_alignment(string1 = nil, string2 = nil) ⇒ Object
# === compare_two_strings_as_alignment.
-
#compseq(i = dna_sequence? ) ⇒ Object
# === compseq.
-
#config? ⇒ Boolean
(also: #configuration?)
# === config? ========================================================================= #.
-
#consider_analysing_the_local_dataset_on_startup ⇒ Object
# === consider_analysing_the_local_dataset_on_startup.
-
#consider_assigning_the_default_dna_sequence_from_a_yaml_file ⇒ Object
# === consider_assigning_the_default_dna_sequence_from_a_yaml_file ========================================================================= #.
-
#considering_changing_the_title_of_the_kde_konsole_tab(to_this_title = 'BioRoebe') ⇒ Object
# === considering_changing_the_title_of_the_kde_konsole_tab ========================================================================= #.
-
#convert_five_prime_dna_into_five_prime_mrna(this_string = sequence? ) ⇒ Object
# === convert_five_prime_dna_into_five_prime_mrna (DNA to mRNA).
-
#copy_bioroebe_shell_before_quitting ⇒ Object
# === copy_bioroebe_shell_before_quitting.
-
#could_this_be_an_amino_acid?(i) ⇒ Boolean
# === could_this_be_an_amino_acid?.
-
#count_amount_of_aminoacids(i) ⇒ Object
# === count_amount_of_aminoacids ========================================================================= #.
-
#create_balanced_composition(i = nil) ⇒ Object
# === create_balanced_composition.
-
#create_fasta_file ⇒ Object
# === create_fasta_file ========================================================================= #.
-
#create_file(i = a?) ) ⇒ Object
# === create_file ========================================================================= #.
-
#create_n_random_amino_acids(n = 1000) ⇒ Object
# === create_n_random_amino_acids ========================================================================= #.
-
#cut(i) ⇒ Object
# === cut (cut tag).
-
#cut_at(this_sequence = 'GAATTC', be_verbose = true) ⇒ Object
# === cut_at.
-
#cut_sequence_in_slices_of(threshold = '9') ⇒ Object
# === cut_sequence_in_slices_of.
-
#cut_with_enzyme(i) ⇒ Object
# === cut_with_enzyme ========================================================================= #.
-
#cutseq(i = [1,3]) ⇒ Object
# === cutseq.
-
#cytosin? ⇒ Boolean
# === cytosin? ========================================================================= #.
-
#dalton(i) ⇒ Object
# === dalton.
-
#deduce_this_aminoacid_sequence(i = 'Lys-Ser-Pro-Ser-Leu-Asn-Ala-Ala-Lys', show_the_rna_sequence = true) ⇒ Object
# === deduce_this_aminoacid_sequence.
-
#default_length? ⇒ Boolean
# === default_length? ========================================================================= #.
-
#design_polylinker(optional_length_of_polylinker = nil, be_verbose = true) ⇒ Object
# === design_polylinker.
-
#designate_this_input_as_coding_entry(i) ⇒ Object
# === designate_this_input_as_coding_entry.
-
#determine_and_report_all_stop_codons ⇒ Object
# === determine_and_report_all_stop_codons ========================================================================= #.
-
#disable(i) ⇒ Object
# === disable (disable tag) ========================================================================= #.
-
#disable_colours_in_an_extended_manner(be_verbose = :be_quiet) ⇒ Object
(also: #disable_enable_colours, #extended_disable_colours)
# === disable_colours_in_an_extended_manner (disable tag) ========================================================================= #.
-
#disable_truncate ⇒ Object
# === disable_truncate ========================================================================= #.
-
#disable_xsel ⇒ Object
# === disable_xsel ========================================================================= #.
-
#discover_all_palindromes(i = dna_sequence?, , min = 4, max = 10) ⇒ Object
# === discover_all_palindromes.
-
#display_all_aminoacids ⇒ Object
# === display_all_aminoacids.
-
#display_glycolysis_pathway ⇒ Object
# === display_glycolysis_pathway.
-
#display_nucleotide_sequence(this_sequence = dna_sequence_object?, , &block) ⇒ Object
(also: #display_this_nucleotide_sequence, #display_this_sequence, #show_this_sequence)
# === display_nucleotide_sequence.
-
#display_open_reading_frames(i = dna_sequence_object?, , &block) ⇒ Object
# === display_open_reading_frames.
-
#dna_padding(this_sequence, get_rid_of_spaces = false) ⇒ Object
(also: #properly_spaced_dna, #properly_padded_dna_string)
# === dna_padding (dna_padding tag).
-
#dna_sequences? ⇒ Boolean
(also: #array_sequences?)
# === dna_sequences? ========================================================================= #.
-
#dna_to_aminoacid_sequence(i = dna_sequence? ) ⇒ Object
# === dna_to_aminoacid_sequence.
-
#dna_translate(i) ⇒ Object
# === dna_translate ========================================================================= #.
-
#dna_with_ends(i = dna_sequence_as_string?, , optional_colourize = nil, colourize_everything = true) ⇒ Object
# === dna_with_ends.
-
#do_a_silent_startup ⇒ Object
(also: #do_silent_startup)
# === do_a_silent_startup.
-
#do_action(*i) ⇒ Object
# === do_action.
-
#do_analyze_sequence(i = sequence? ) ⇒ Object
# === do_analyze_sequence.
-
#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.
-
#do_not_show_the_leader(be_verbose = true) ⇒ Object
# === do_not_show_the_leader ========================================================================= #.
-
#do_not_show_the_trailer(be_verbose = true) ⇒ Object
# === do_not_show_the_trailer ========================================================================= #.
-
#do_not_truncate ⇒ Object
# === do_not_truncate ========================================================================= #.
-
#do_not_use_working_directory_as_prompt ⇒ Object
# === do_not_use_working_directory_as_prompt ========================================================================= #.
-
#do_open(i) ⇒ Object
# === do_open.
-
#do_quit(determine_what_to_do = exit_the_shell_how? ) ⇒ Object
# === do_quit (exit tag, quit tag).
-
#do_start_the_sinatra_interface ⇒ Object
# === do_start_the_sinatra_interface.
-
#do_toggle_debug_value ⇒ Object
# === do_toggle_debug_value ========================================================================= #.
-
#do_truncate? ⇒ Boolean
# === do_truncate? ========================================================================= #.
-
#do_use_working_directory_as_prompt ⇒ Object
(also: #use_working_directory_as_prompt)
# === use_working_directory_as_prompt.
-
#does_this_remote_file_exist?(i) ⇒ Boolean
# === does_this_remote_file_exist?.
-
#downcase_main_string ⇒ Object
# === downcase_main_string (downcase tag, dcase tag).
-
#download(i) ⇒ Object
# === download (download tag).
-
#download_fasta(i = nil) ⇒ Object
# === download_fasta.
-
#download_this_pdb_file(i = '3O30') ⇒ Object
# === download_this_pdb_file.
-
#dump(optional_arguments = nil) ⇒ Object
# === dump.
-
#e(i = '') ⇒ Object
# === e (e tag) ========================================================================= #.
-
#ee(i) ⇒ Object
# === ee (ee tag).
-
#efetch(i) ⇒ Object
# === efetch.
-
#enable(i) ⇒ Object
(also: #use)
# === enable (enable tag).
-
#enable_colours_in_an_extended_manner(be_verbose = :be_quiet) ⇒ Object
(also: #extended_enable_colours)
# === enable_colours_in_an_extended_manner (enable tag).
-
#enable_configuration ⇒ Object
# === enable_configuration ========================================================================= #.
-
#enable_gtk ⇒ Object
# === enable_gtk.
-
#enable_gtk_section_antisensestrand ⇒ Object
# === enable_gtk_section_antisensestrand ========================================================================= #.
-
#enable_xsel ⇒ Object
# === enable_xsel ========================================================================= #.
-
#ensure_that_the_bioshell_log_directory_exists ⇒ Object
# === ensure_that_the_bioshell_log_directory_exists ========================================================================= #.
-
#enter_base_directory ⇒ Object
# === enter_base_directory.
-
#enter_the_main_loop ⇒ Object
(also: #loop_get_user_input, #enter_main_loop)
# === enter_the_main_loop (loop tag).
-
#ereturn(i = '') ⇒ Object
# === ereturn ========================================================================= #.
-
#erev(i = '') ⇒ Object
# === erev (erev tag).
-
#exit_the_shell_how? ⇒ Boolean
# === exit_the_shell_how? ========================================================================= #.
-
#extract_sequence_from_this_file(i) ⇒ Object
(also: #extract_sequence)
# === extract_sequence_from_this_file.
-
#fasta? ⇒ Boolean
(also: #last_fasta?, #last_fasta_entry?)
# === fasta?.
-
#fasta_file?(i = :fasta_file) ⇒ Boolean
# === fasta_file? ========================================================================= #.
-
#feedback_version ⇒ Object
# === feedback_version ========================================================================= #.
-
#feedback_where_files_are_kept_locally ⇒ Object
# === feedback_where_files_are_kept_locally.
-
#feedback_whether_we_are_in_debug_mode ⇒ Object
# === feedback_whether_we_are_in_debug_mode ========================================================================= #.
-
#feedback_whether_we_will_also_set_the_xorg_buffer ⇒ Object
# === feedback_whether_we_will_also_set_the_xorg_buffer ========================================================================= #.
-
#fetch_from_pdb(i) ⇒ Object
# === fetch_from_pdb.
-
#file_dna_string_saved? ⇒ Boolean
# === file_dna_string_saved? ========================================================================= #.
-
#find_all_orfs(i = dna_sequence? ) ⇒ Object
# === find_all_orfs.
-
#find_complementary_strand(i = dna_sequence? ) ⇒ Object
(also: #show_complementary_strand)
# === find_complementary_strand.
-
#find_gene(i = :default) ⇒ Object
# === find_gene.
-
#find_kdel_sequence ⇒ Object
# === find_kdel_sequence ========================================================================= #.
-
#find_longest_substring(i = dna_string?) ) ⇒ Object
# === find_longest_substring ========================================================================= #.
-
#find_longest_substring_via_LCS(i) ⇒ Object
# === find_longest_substring_via_LCS.
-
#find_restriction_enzymes_that_cut_at(i) ⇒ Object
# === find_restriction_enzymes_that_cut_at.
-
#find_restriction_sites(i = string?) ) ⇒ Object
# === find_restriction_sites.
-
#find_shine_dalgarno_sequence(i = dna_sequence_as_string? ) ⇒ Object
# === find_shine_dalgarno_sequence.
-
#first(i) ⇒ Object
# === first ========================================================================= #.
-
#first_argument? ⇒ Boolean
(also: #f?, #f)
# === first_argument? ========================================================================= #.
-
#format_this_nucleotide_sequence(i, &block) ⇒ Object
# === format_this_nucleotide_sequence.
-
#freeze_the_main_sequence ⇒ Object
# === freeze_the_main_sequence ========================================================================= #.
-
#generate_palindrome(i) ⇒ Object
# === generate_palindrome.
-
#generate_pdf_tutorial ⇒ Object
# === generate_pdf_tutorial.
-
#generate_random_dna_sequence_with_variable_length_and_variable_composition ⇒ Object
# === generate_random_dna_sequence_with_variable_length_and_variable_composition.
-
#generate_random_protein_sequence_with_variable_length_and_variable_composition ⇒ Object
# === generate_random_protein_sequence_with_variable_length_and_variable_composition.
-
#generate_single_sequence_repeats ⇒ Object
# === generate_single_sequence_repeats.
-
#get_long_name_of_amino_acid(i) ⇒ Object
# === get_long_name_of_amino_acid ========================================================================= #.
-
#guanin? ⇒ Boolean
# === guanin? ========================================================================= #.
-
#handle_fasta(i) ⇒ Object
(also: #assign_fasta, #handle_this_fasta_file)
# === handle_fasta.
-
#handle_pdb_files(i) ⇒ Object
# === handle_pdb_files.
-
#handle_this_file(this_file) ⇒ Object
# === handle_this_file.
-
#highlight_colour? ⇒ Boolean
(also: #yellow)
# === highlight_colour?.
-
#identify_aminoacid(i) ⇒ Object
# === identify_aminoacid.
-
#include?(i) ⇒ Boolean
# === include?.
-
#index_this_fasta_file(i) ⇒ Object
# === index_this_fasta_file.
-
#initialize(commandline_arguments = ARGV, run_already = true) ⇒ Shell
constructor
# === initialize ========================================================================= #.
-
#initialize_clipboard ⇒ Object
# === initialize_clipboard ========================================================================= #.
-
#initialize_main_sequence(n_nucleotides = 250) ⇒ Object
(also: #reset_string)
# === initialize_main_sequence.
-
#initialize_the_user_input_specific_variables ⇒ Object
# === initialize_the_user_input_specific_variables ========================================================================= #.
-
#install(i) ⇒ Object
# === install (install tag) ========================================================================= #.
-
#interactive_colour_menu ⇒ Object
# === interactive_colour_menu ========================================================================= #.
-
#interactive_use_of_levensthein(i = all_arguments? ) ⇒ Object
# === interactive_use_of_levensthein ========================================================================= #.
-
#interactively_pick_colour ⇒ Object
# === interactively_pick_colour.
-
#is_a_registered_compound?(i) ⇒ Boolean
# === is_a_registered_compound? ========================================================================= #.
-
#is_a_stop_codon?(i) ⇒ Boolean
# === is_a_stop_codon? ========================================================================= #.
-
#is_any_nucleotide_assigned? ⇒ Boolean
# === is_any_nucleotide_assigned? ========================================================================= #.
-
#is_dna? ⇒ Boolean
# === is_dna? ========================================================================= #.
-
#is_palindrome?(i) ⇒ Boolean
# === is_palindrome? ========================================================================= #.
-
#is_the_main_sequence_frozen? ⇒ Boolean
(also: #the_main_sequence_is_frozen?)
# === is_the_main_sequence_frozen? ========================================================================= #.
-
#is_this_a_cd_alias?(i) ⇒ Boolean
# === is_this_a_cd_alias?.
-
#is_this_a_valid_codon?(i) ⇒ Boolean
# === is_this_a_valid_codon?.
-
#last_inputted_command?(array_history = array_history? ) ⇒ Boolean
# === last_inputted_command?.
-
#leading_3_prime ⇒ Object
(also: #leading_three_prime, #leading_3)
# === leading_3_prime.
-
#leading_5_prime(get_rid_of_spaces = false) ⇒ Object
(also: #five_prime, #leading_five_prime, #leader, #lead_five_prime, #return_five_prime_header, #leading_five, #five_leader?)
# === leading_5_prime.
-
#left_chop(i) ⇒ Object
# === left_chop ========================================================================= #.
-
#list(i = nil) ⇒ Object
# === list ========================================================================= #.
-
#load(i = file_dna_string_saved? ) ⇒ Object
(also: #load_dataset_from)
# === load (load tag).
-
#load_dna ⇒ Object
# === load_dna.
-
#load_gtk ⇒ Object
# === load_gtk.
-
#load_gtk3_component_aminoacid_composition ⇒ Object
# === load_gtk3_component_aminoacid_composition ========================================================================= #.
-
#load_my_file ⇒ Object
# === load_my_file (load tag).
-
#log_user_input? ⇒ Boolean
# === log_user_input?.
-
#main_colour ⇒ Object
(also: #main_col)
# === main_colour ========================================================================= #.
-
#mass_weight(i = aminoacids?, , be_verbose = true) ⇒ Object
# === mass_weight (mass_weight tag).
-
#may_we_show_the_startup_information? ⇒ Boolean
# === may_we_show_the_startup_information? ========================================================================= #.
-
#menu(i = command_to_be_passed_to_the_menu?, , report_if_we_did_not_find_the_command = true) ⇒ Object
# === menu (menu tag) ========================================================================= #.
-
#mirror_repeat(i = dna_sequence? ) ⇒ Object
# === mirror_repeat ========================================================================= #.
-
#mode? ⇒ Boolean
# === mode? ========================================================================= #.
-
#molecular_mass_of(i = aminoacids?, , optional_round_here = nil) ⇒ Object
# === molecular_mass_of.
-
#molecular_mass_of_amino_acids_in_the_sequence(i = aminoacid_sequence? ) ⇒ Object
(also: #molecular_mass_of_amino_acids_in_this_sequence)
# === molecular_mass_of_amino_acids_in_the_sequence.
-
#move_file_to_its_correct_location(i) ⇒ Object
# === move_file_to_its_correct_location ========================================================================= #.
-
#mutate_aminoacid_position(this_position = 1) ⇒ Object
# === mutate_aminoacid_position.
-
#mutate_dna_sequence(n_times = 1, old_sequence = dna_sequence? ) ⇒ Object
# === mutate_dna_sequence.
-
#mutate_position(nucleotide_position, mutate_to_this_nucleotide = return_random_nucleotide) ⇒ Object
# === mutate_position.
-
#n_uracil? ⇒ Boolean
# === n_uracil? ========================================================================= #.
-
#name_of_gene? ⇒ Boolean
# === name_of_gene? ========================================================================= #.
-
#ncbi_nucleotide_search_for(i = '') ⇒ Object
# === ncbi_nucleotide_search_for ========================================================================= #.
-
#no_newlines(this_file) ⇒ Object
# === no_newlines.
-
#notify_the_user_as_to_how_findgene_works ⇒ Object
# === notify_the_user_as_to_how_findgene_works ========================================================================= #.
-
#nucleotide_sequence? ⇒ Boolean
(also: #dna_sequence?, #dna_string?, #dna_seq?, #string?, #main_string?, #seq?, #sequence_1, #seq1, #seq1?)
# === nucleotide_sequence? (string? tag).
-
#nucleotides_or_aminoacids? ⇒ Boolean
# === nucleotides_or_aminoacids? ========================================================================= #.
-
#obtain_current_prompt ⇒ Object
# === obtain_current_prompt.
-
#obtain_current_prompt_while_honouring_colours ⇒ Object
# === obtain_current_prompt_while_honouring_colours ========================================================================= #.
-
#obtain_multiline_fasta ⇒ Object
# === obtain_multiline_fasta.
-
#obtain_url_for(i) ⇒ Object
# === obtain_url_for ========================================================================= #.
-
#obtain_user_input ⇒ Object
(also: #get_user_input, #read_user_input)
# === obtain_user_input (input tag).
-
#only_nucleotides?(i) ⇒ Boolean
# === only_nucleotides?.
-
#only_valid_nucleotides?(i) ⇒ Boolean
(also: #only_valid_dna_nucleotides?)
# === only_valid_nucleotides?.
-
#open_1igt_in_the_browser ⇒ Object
# === open_1igt_in_the_browser ========================================================================= #.
-
#open_blast_webpage ⇒ Object
open_blast_webpage ========================================================================= #.
-
#open_expasy(i = all_arguments?) ) ⇒ Object
# === open_expasy ========================================================================= #.
-
#open_in_uniprot(i = 'A1XPA3') ⇒ Object
# === open_in_uniprot.
-
#open_my_files ⇒ Object
# === open_my_files (open tag, files tag).
-
#open_this_file_in_editor(file) ⇒ Object
# === open_this_file_in_editor (editor tag) ========================================================================= #.
-
#open_this_ncbi_page(i) ⇒ Object
# === open_this_ncbi_page.
-
#original_input? ⇒ Boolean
(also: #original_input)
# === original_input? ========================================================================= #.
-
#padding? ⇒ Boolean
(also: #pad, #pad?, #lpad?, #left_pad?, #left_padding?, #default_padding)
# === padding? (padding tag).
-
#parse(i) ⇒ Object
# === parse (parse tag) ========================================================================= #.
-
#parse_fasta_format(i = nil) ⇒ Object
(also: #parse_this_fasta_file)
# === parse_fasta_format.
-
#parse_this_fasta_sequence(i) ⇒ Object
# === parse_this_fasta_sequence ========================================================================= #.
-
#parse_this_gff_file(i) ⇒ Object
# === parse_this_gff_file.
-
#parse_this_pdb_file(i) ⇒ Object
# === parse_this_pdb_file ========================================================================= #.
-
#parse_this_user_input(i) ⇒ Object
# === parse_this_user_input.
-
#perform_a_pubmed_search(i) ⇒ Object
# === perform_a_pubmed_search ========================================================================= #.
-
#perform_frameshift_action(i) ⇒ Object
# === perform_frameshift_action.
-
#perform_startup_actions ⇒ Object
# === perform_startup_actions (startup tag).
-
#permanently_disable_startup_intro ⇒ Object
# === permanently_disable_startup_intro.
-
#prepend(i) ⇒ Object
# === prepend.
-
#primer(i) ⇒ Object
# === primer? ========================================================================= #.
-
#print_aa_table(optional_arguments = all_arguments?) ) ⇒ Object
# === print_aa_table.
-
#print_aminoacid_information_table ⇒ Object
# === print_aminoacid_information_table.
-
#print_rev ⇒ Object
# === print_rev ========================================================================= #.
-
#protein_stats ⇒ Object
# === protein_stats ========================================================================= #.
-
#pubmed(number = 125512) ⇒ Object
# === pubmed.
-
#punnet(i) ⇒ Object
# === punnet.
-
#purge(i) ⇒ Object
# === purge.
-
#random(n_elements = default_length?, , dna_or_amino_acid = :dna, do_report_the_sequence = false) ⇒ Object
# === random (random tag, rand tag).
-
#random_dna_sequence(length = 250) ⇒ Object
# === random_dna_sequence.
-
#random_insert(i) ⇒ Object
# === random_insert.
-
#raw_aminoacid_sequence? ⇒ Boolean
(also: #aminoacids?, #amino_acid_sequence?, #aminoacid_sequence?, #aa_sequence?, #aa?)
# === raw_aminoacid_sequence?.
-
#raw_sequence? ⇒ Boolean
(also: #dna_sequence_as_string?, #dna_sequence_object_as_string?, #sequence_as_string?)
# === raw_sequence?.
-
#readline_is_available? ⇒ Boolean
(also: #use_readline?, #has_readline?)
# === readline_is_available? ========================================================================= #.
-
#register_this_download(i) ⇒ Object
# === register_this_download.
-
#remaining_arguments? ⇒ Boolean
# === remaining_arguments? ========================================================================= #.
-
#remove_question_mark? ⇒ Boolean
# === remove_question_mark? ========================================================================= #.
-
#remove_sequence(i) ⇒ Object
(also: #remove)
# === remove_sequence.
-
#remove_trailing_escape_code(i) ⇒ Object
# === remove_trailing_escape_code ========================================================================= #.
-
#replay(i = nil) ⇒ Object
# === replay ========================================================================= #.
-
#report_all_stop_codons(i = dna_sequence_object? ) ⇒ Object
# === report_all_stop_codons.
-
#report_colourized_sequence(colourize_what = :start_and_stop_codon) ⇒ Object
# === report_colourized_sequence.
-
#report_current_genbank_version(optional_arguments = nil) ⇒ Object
# === report_current_genbank_version.
-
#report_current_working_directory ⇒ Object
# === report_current_working_directory ========================================================================= #.
-
#report_everything_about_this_amino_acid(i) ⇒ Object
# === report_everything_about_this_amino_acid.
-
#report_five_prime_three_prime(i) ⇒ Object
# === report_five_prime_three_prime ========================================================================= #.
-
#report_how_many_aminoacids_we_have ⇒ Object
# === report_how_many_aminoacids_we_have.
-
#report_main_sequence(input = dna_sequence_as_string?, , colourize = nil) ⇒ Object
(also: #show_main_sequence, #show_colourized_sequence, #show_dna_sequence, #show_DNA_sequence)
# === report_main_sequence.
-
#report_mode ⇒ Object
# === report_mode ========================================================================= #.
-
#report_n_proteins_registered_in_swiss_prot ⇒ Object
# === report_n_proteins_registered_in_swiss_prot.
-
#report_n_start_codons(this_string = string?, , use_this_as_start_codon = :default, in_which_frame = :frame1) ⇒ Object
# === report_n_start_codons.
-
#report_size_of(i = nil) ⇒ Object
# === report_size_of ========================================================================= #.
-
#report_size_of_main_string(i = dna_sequence_object?, , type_of_string = 'main ') ⇒ Object
(also: #report_length_of_the_dna_string, #report_size_of_this_sequence)
# === report_size_of_main_string ========================================================================= #.
-
#report_syntax_help_for_frameshift_action ⇒ Object
# === report_syntax_help_for_frameshift_action ========================================================================= #.
-
#report_that_a_string_must_be_assigned_first ⇒ Object
# === report_that_a_string_must_be_assigned_first ========================================================================= #.
-
#report_that_the_main_sequence_is_frozen ⇒ Object
# === report_that_the_main_sequence_is_frozen ========================================================================= #.
-
#report_the_first_atg ⇒ Object
# === report_the_first_atg.
-
#report_the_protein_weight ⇒ Object
# === report_the_protein_weight ========================================================================= #.
-
#report_this_dna_sequence_with_proper_trailer_and_leader(i) ⇒ Object
# === report_this_dna_sequence_with_proper_trailer_and_leader ========================================================================= #.
-
#report_this_input_was_not_found(i = '') ⇒ Object
# === report_this_input_was_not_found.
-
#report_useful_packages_installed ⇒ Object
# === report_useful_packages_installed.
-
#report_when_the_bioroebe_project_was_last_updated ⇒ Object
# === report_when_the_bioroebe_project_was_last_updated ========================================================================= #.
-
#report_where_the_home_directory_can_be_found(i = log_dir? ) ⇒ Object
# === report_where_the_home_directory_can_be_found ========================================================================= #.
-
#report_where_the_pdf_tutorial_can_be_found ⇒ Object
# === report_where_the_pdf_tutorial_can_be_found.
-
#report_where_we_store ⇒ Object
# === report_where_we_store ========================================================================= #.
-
#report_whether_readline_is_available ⇒ Object
# === report_whether_readline_is_available ========================================================================= #.
-
#report_whether_we_will_make_use_of_expand_cd_aliases ⇒ Object
# === report_whether_we_will_make_use_of_expand_cd_aliases ========================================================================= #.
-
#report_which_yaml_engine_is_in_use ⇒ Object
# === report_which_yaml_engine_is_in_use ========================================================================= #.
-
#reset(be_verbose = true) ⇒ Object
# === reset (reset tag) ========================================================================= #.
-
#reset_the_user_input_specific_variables ⇒ Object
# === reset_the_user_input_specific_variables ========================================================================= #.
-
#reset_to_the_initial_state(be_verbose = true) ⇒ Object
(also: #reset_to_the_internal_state)
# === reset_to_the_initial_state ========================================================================= #.
-
#restore_default_prompt ⇒ Object
# === restore_default_prompt ========================================================================= #.
-
#restore_the_last_chop_operation ⇒ Object
# === restore_the_last_chop_operation.
-
#restriction_enzyme_digest(split_at = nil) ⇒ Object
(also: #digest)
# === restriction_enzyme_digest.
-
#restriction_enzymes_run ⇒ Object
# === restriction_enzymes_run ========================================================================= #.
-
#result? ⇒ Boolean
# === result? ========================================================================= #.
-
#return_a_random_sequence_of_n_nucleotides(i = 250) ⇒ Object
# === return_a_random_sequence_of_n_nucleotides ========================================================================= #.
-
#return_all_genes ⇒ Object
# === return_all_genes ========================================================================= #.
-
#return_available_vectors ⇒ Object
# === return_available_vectors ========================================================================= #.
-
#return_complement(i = dna_sequence? ) ⇒ Object
(also: #complement, #complement_sequence?, #reverse)
# === return_complement.
-
#return_default_GFP_sequence(path_to_the_file = FILE_GFP_SEQUENCE) ⇒ Object
# === return_default_GFP_sequence ========================================================================= #.
-
#return_dna_nucleotides ⇒ Object
# === return_dna_nucleotides.
-
#return_dna_sequence_as_sequence_object ⇒ Object
(also: #main_sequence?, #dna_sequence_object?, #sequence_object?, #sequence?, #seq_object?, #sequence, #seq_obj?, #last_nucleotide_sequence?)
# === return_dna_sequence_as_sequence_object.
-
#return_fasta_files_in_the_log_directory ⇒ Object
# === return_fasta_files_in_the_log_directory ========================================================================= #.
-
#return_pwd ⇒ Object
(also: #return_default_prompt)
# === return_pwd ========================================================================= #.
-
#return_random_aminoacid ⇒ Object
# === return_random_aminoacid ========================================================================= #.
-
#return_random_nucleotide ⇒ Object
(also: #add_nucleotide)
# === return_random_nucleotide.
-
#return_random_restriction_enzyme(be_verbose = false) ⇒ Object
# === return_random_restriction_enzyme.
-
#return_reverse_dna_string ⇒ Object
# === return_reverse_dna_string ========================================================================= #.
-
#return_sequence_from_this_number(i = 1) ⇒ Object
# === return_sequence_from_this_number ========================================================================= #.
-
#reverse_complement(i = sequence? ) ⇒ Object
# === reverse_complement (reverse complement tag).
-
#run ⇒ Object
# === run ========================================================================= #.
-
#run_in_GUI_mode? ⇒ Boolean
(also: #run_as_GUI?, #run_in_GUI_settings?, #run_in_GUI_setting?)
# === run_in_GUI_mode? ========================================================================= #.
-
#run_nls_search ⇒ Object
# === run_nls_search.
-
#run_sizeseq ⇒ Object
# === run_sizeseq.
-
#run_sql_query(i, be_verbose = true, optional_append_this = '') ⇒ Object
(also: #sql_query, #run_query, #run_sql)
# === run_sql_query ========================================================================= #.
-
#run_this_user_input ⇒ Object
# === menu (menu tag) ========================================================================= # === run_this_user_input().
-
#runmode_is_commandline? ⇒ Boolean
# === runmode_is_commandline? ========================================================================= #.
-
#salt_adjusted_tm(i) ⇒ Object
# === salt_adjusted_tm ========================================================================= #.
-
#sanitize_input(i) ⇒ Object
# === sanitize_input.
-
#sanitize_nucleotide_sequence(i) ⇒ Object
# === sanitize_nucleotide_sequence.
-
#save_file? ⇒ Boolean
# === save_file? ========================================================================= #.
-
#save_history_to_file(dataset = ) ⇒ Object
# === save_history_to_file.
-
#save_my_file(&block) ⇒ Object
# === save_my_file (save tag).
-
#say_goodbye ⇒ Object
# === say_goodbye ========================================================================= #.
-
#scan_for_gff_files ⇒ Object
# === scan_for_gff_files ========================================================================= #.
-
#scan_for_leucine_zippers(i = amino_acid_sequence? ) ⇒ Object
# === scan_for_leucine_zippers.
-
#scan_or_parse_for_this_gff_file_or_any_gff_file(i) ⇒ Object
# === scan_or_parse_for_this_gff_file_or_any_gff_file ========================================================================= #.
-
#search_for(i, be_verbose = true) ⇒ Object
# === search_for (search_for tag).
-
#search_for? ⇒ Boolean
# === search_for?.
-
#search_for_known_promoters ⇒ Object
# === search_for_known_promoters.
-
#search_for_nucleotide_sequence(i) ⇒ Object
# === search_for_nucleotide_sequence.
-
#search_for_tata_consensus_sequence ⇒ Object
# === search_for_tata_consensus_sequence.
-
#search_sequence_for_open_reading_frames(i = :default, use_which_frame = :frame1, use_this_start_codon = :default) ⇒ Object
# === search_sequence_for_open_reading_frames.
-
#second_argument? ⇒ Boolean
(also: #second_argument)
# === second_argument? ========================================================================= #.
-
#sequence_2 ⇒ Object
(also: #seq2, #seq2?)
# === sequence2 ========================================================================= #.
-
#sequence_3 ⇒ Object
(also: #seq3, #seq3?)
# === sequence3 ========================================================================= #.
-
#sequence_4 ⇒ Object
(also: #seq4, #seq4?)
# === sequence4 ========================================================================= #.
-
#sequence_5 ⇒ Object
(also: #seq5, #seq5?)
# === sequence5 ========================================================================= #.
-
#sequence_6 ⇒ Object
(also: #seq6, #seq6?)
# === sequence6 ========================================================================= #.
-
#set_aminoacids(i = :random, how_many_to_generate = :default, be_verbose = true) ⇒ Object
(also: #assign_aminoacid_sequence, #assign_protein_sequence, #set_aminoacid_sequence)
# === set_aminoacids (assign protein tag, set aminoacids tag).
-
#set_codon_table(i) ⇒ Object
# === set_codon_table.
-
#set_default_highlight_colour ⇒ Object
# === set_default_highlight_colour ========================================================================= #.
-
#set_default_length(i = DEFAULT_LENGTH_FOR_DNA, be_verbose = false) ⇒ Object
(also: #set_maxlength)
# === set_default_length ========================================================================= #.
-
#set_download_directory(i = ::Bioroebe.log_dir?) ⇒ Object
# === set_download_directory ========================================================================= #.
-
#set_exit_gracefully ⇒ Object
# === set_exit_gracefully ========================================================================= #.
-
#set_highlight_colour(i = :violet, be_verbose = false) ⇒ Object
# === set_highlight_colour.
-
#set_highlight_colour_or_search_for_this_sequence(i, be_verbose = false) ⇒ Object
# === set_highlight_colour_or_search_for_this_sequence ========================================================================= #.
-
#set_jumper_directory(i) ⇒ Object
# === set_jumper_directory ========================================================================= #.
-
#set_locus(i) ⇒ Object
# === set_locus ========================================================================= #.
-
#set_log_dir(i = first_argument? ) ⇒ Object
# === set_log_dir ========================================================================= #.
-
#set_mode(i = :dna) ⇒ Object
# === set_mode ========================================================================= #.
-
#set_name_of_gene(i = '', be_verbose = :be_verbose) ⇒ Object
# === set_name_of_gene.
-
#set_nucleotide_sequence(i = nil, be_verbose = false, do_upcase = :check_for_config_value_here, &block) ⇒ Object
(also: #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).
-
#set_padding(i = DEFAULT_PADDING, be_verbose = :be_quiet) ⇒ Object
# === set_padding.
-
#set_random_aminoacids ⇒ Object
# === set_random_aminoacids.
-
#set_result(i) ⇒ Object
# === set_result ========================================================================= #.
-
#set_save_file(i = :default) ⇒ Object
# === set_save_file ========================================================================= #.
-
#set_search_for(i, be_verbose = true) ⇒ Object
(also: #set_search_string)
# === set_search_for.
-
#set_sequence_2(i = '') ⇒ Object
# === set_sequence_2 ========================================================================= #.
-
#set_sequence_3(i = '') ⇒ Object
# === set_sequence_3 ========================================================================= #.
-
#set_sequence_4(i = '') ⇒ Object
# === set_sequence_4 ========================================================================= #.
-
#set_sequence_5(i = '') ⇒ Object
# === set_sequence_5 ========================================================================= #.
-
#set_sequence_6(i = '') ⇒ Object
# === set_sequence_6 ========================================================================= #.
-
#set_start_codon(i = nil) ⇒ Object
# === set_start_codon.
-
#set_use_this_prompt(i = NAME_OF_BIO_SHELL) ⇒ Object
(also: #set_prompt)
# === set_use_this_prompt.
-
#set_user_input(i) ⇒ Object
# === set_user_input ========================================================================= #.
-
#set_xclip(i = dna_string? ) ⇒ Object
# === set_xclip (xclip tag, xorg tag, buffer tag).
-
#setup_readline ⇒ Object
# === setup_readline.
-
#shorten_aminoacid(these_aminoacids = aminoacid_sequence? ) ⇒ Object
# === shorten_aminoacid.
-
#show(i) ⇒ Object
# === show (show tag).
-
#show_2D_dotplot(string1 = nil, string2 = nil) ⇒ Object
# === show_2D_dotplot ========================================================================= #.
-
#show_agarose_table ⇒ Object
# === show_agarose_table.
-
#show_all_codon_tables(show_what = :everything) ⇒ Object
# === show_all_codon_tables.
-
#show_all_deducible_aminoacid_sequences(i = dna_sequence_as_string?, , also_show_numbers = true, show_translations_aligned = true) ⇒ Object
# === show_all_deducible_aminoacid_sequences.
-
#show_all_dmp_files ⇒ Object
# === show_all_dmp_files.
-
#show_all_pathways ⇒ Object
# === show_all_pathways.
-
#show_all_yaml_files ⇒ Object
# === show_all_yaml_files.
-
#show_alu_sequence ⇒ Object
# === show_alu_sequence.
-
#show_aminoacid_sequence ⇒ Object
# === show_aminoacid_sequence.
-
#show_aminoacids_mass_table ⇒ Object
(also: #aminoacid_table_overview)
# === show_aminoacids_mass_table.
-
#show_aminoacids_residues ⇒ Object
# === show_aminoacids_residues ========================================================================= #.
-
#show_and_calculate_weight_of_dna_string(i = dna_sequence_object? ) ⇒ Object
# === show_and_calculate_weight_of_dna_string ========================================================================= #.
-
#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 ========================================================================= #.
-
#show_available_vectors ⇒ Object
# === show_available_vectors ========================================================================= #.
-
#show_average_weight_of_a_nucleotide ⇒ Object
# === show_average_weight_of_a_nucleotide.
-
#show_average_weight_of_an_aminoacid ⇒ Object
# === show_average_weight_of_an_aminoacid.
-
#show_blosum_matrix ⇒ Object
# === show_blosum_matrix.
-
#show_both_dna_strands ⇒ Object
(also: #show_double_strand)
# === show_double_strand ========================================================================= #.
-
#show_ccaat_sites(search_for_this_sequence = 'CCAAT') ⇒ Object
(also: #show_CCAAT_sites)
# === show_ccaat_sites.
-
#show_chromosome_table ⇒ Object
# === show_chromosome_table ========================================================================= #.
-
#show_codon_piped_sequence ⇒ Object
# === show_codon_piped_sequence ========================================================================= #.
-
#show_codon_table(i = nil) ⇒ Object
# === show_codon_table ========================================================================= #.
-
#show_codon_usage(i = dna_sequence_as_string? ) ⇒ Object
# === show_codon_usage.
-
#show_codons_of_this_aminoacid_or_show_kazusa_codon(i = nil) ⇒ Object
# === show_codons_of_this_aminoacid_or_show_kazusa_codon.
-
#show_commandline_options ⇒ Object
# === show_commandline_options.
-
#show_complement(i = dna_string?, , also_include_prime_ends = false) ⇒ Object
# === show_complement.
-
#show_composition(i = dna_string? ) ⇒ Object
# === show_composition.
-
#show_config_dir ⇒ Object
# === show_config_dir.
-
#show_copyright_clause ⇒ Object
# === show_copyright_clause.
-
#show_cpg_islands ⇒ Object
# === show_cpg_islands.
-
#show_date ⇒ Object
# === show_date ========================================================================= #.
-
#show_directory_content(of_this_dir = '*') ⇒ Object
# === show_directory_content ========================================================================= #.
-
#show_disulfides ⇒ Object
# === show_disulfides.
-
#show_dna_string(this_string = dna_string?, , truncate_too_long_result = do_truncate? ) ⇒ Object
(also: #show_main_string, #report_sequence, #show_sequence, #show_main_dna_sequence, #show_string)
# === show_dna_string (show string tag, show tag).
-
#show_download_dir ⇒ Object
# === show_download_dir ========================================================================= #.
-
#show_Ecoli_K12_information ⇒ Object
# === show_Ecoli_K12_information ========================================================================= #.
-
#show_editor_in_use ⇒ Object
# === show_editor_in_use ========================================================================= #.
-
#show_fasta_headers(i) ⇒ Object
# === show_fasta_headers.
-
#show_fastq_quality_score_table(_ = Bioroebe.file_fastq_quality_schemes) ⇒ Object
# === show_fastq_quality_score_table.
-
#show_file_listing(from_this_directory = Dir.pwd) ⇒ Object
# === show_file_listing.
-
#show_first_orf(of_this_sequence = dna_sequence_object? ) ⇒ Object
# === show_first_orf.
-
#show_GFP_sequence ⇒ Object
# === show_GFP_sequence (gfp tag).
-
#show_header_of(i) ⇒ Object
# === show_header_of ========================================================================= #.
-
#show_header_of_this_pdb_file(i) ⇒ Object
# === show_header_of_this_pdb_file ========================================================================= #.
-
#show_help(optional_arguments = nil) ⇒ Object
# === show_help (help tag, he tag).
-
#show_hint_how_to_use_the_local_sequences ⇒ Object
# === show_hint_how_to_use_the_local_sequences.
-
#show_histone_table ⇒ Object
# === show_histone_table ========================================================================= #.
-
#show_history ⇒ Object
# === show_history (history tag).
-
#show_how_to_use_the_names_for_the_taxonomy_table ⇒ Object
# === show_how_to_use_the_names_for_the_taxonomy_table ========================================================================= #.
-
#show_html_colours ⇒ Object
# === show_html_colours ========================================================================= #.
-
#show_human_genome_version(remote_URL = 'https://www.ensembl.org/Homo_sapiens/Info/Index') ⇒ Object
# === show_human_genome_version.
-
#show_hydropathy_table ⇒ Object
# === show_hydropathy_table.
-
#show_information_about_the_gff_format ⇒ Object
# === show_information_about_the_gff_format ========================================================================= #.
-
#show_insulin_entries_at_NCBI ⇒ Object
# === show_insulin_entries_at_NCBI ========================================================================= #.
-
#show_jumper_directories ⇒ Object
# === show_jumper_directories ========================================================================= #.
-
#show_known_nls_sequences ⇒ Object
# === show_known_nls_sequences.
-
#show_last_downloaded_file ⇒ Object
# === show_last_downloaded_file ========================================================================= #.
-
#show_last_input ⇒ Object
# === show_last_input.
-
#show_length_of_alpha_helix(i) ⇒ Object
# === show_length_of_alpha_helix ========================================================================= #.
-
#show_local_sequences ⇒ Object
# === show_local_sequences.
-
#show_log_dir ⇒ Object
# === show_log_dir ========================================================================= #.
-
#show_mnemo ⇒ Object
# === show_mnemo.
-
#show_molweight(use_cliner = true) ⇒ Object
# === show_molweight ========================================================================= #.
-
#show_my_fasta_file ⇒ Object
# === show_my_fasta_file ========================================================================= #.
-
#show_name_of_the_gene ⇒ Object
# === show_name_of_the_gene ========================================================================= #.
-
#show_nucleotide_sequence? ⇒ Boolean
(also: #display_nucleotide_object?)
# === show_nucleotide_sequence? ========================================================================= #.
-
#show_nucleotides_table ⇒ Object
# === show_nucleotides_table.
-
#show_numbered_nucleotide_positions(_ = sequence?.string?) ⇒ Object
# === show_numbered_nucleotide_positions.
-
#show_oligo_length_three(sequence = dna_sequence_object? ) ⇒ Object
# === show_oligo_length_three.
-
#show_oligo_length_two(string = string? ) ⇒ Object
# === show_oligo_length_two.
-
#show_ori_sequences ⇒ Object
# === show_ori_sequences.
-
#show_position_for_the_main_sequence ⇒ Object
# === show_position_for_the_main_sequence ========================================================================= #.
-
#show_position_of_sequence(i = aa_sequence?, , chunk_size = 10) ⇒ Object
# === show_position_of_sequence.
-
#show_possible_codons_for_this_aminoacid(i) ⇒ Object
# === show_possible_codons_for_this_aminoacid ========================================================================= #.
-
#show_possible_phosphorylation_sites(i = aminoacid_sequence?) ) ⇒ Object
# === show_possible_phosphorylation_sites.
-
#show_protein_composition(i) ⇒ Object
# === show_protein_composition.
-
#show_readline_completions ⇒ Object
# === show_readline_completions ========================================================================= #.
-
#show_resources_about_the_horseradish_peroxidase ⇒ Object
# === show_resources_about_the_horseradish_peroxidase ========================================================================= #.
-
#show_reste ⇒ Object
# === show_reste.
-
#show_restriction_enzymes(optional_input = nil) ⇒ Object
# === show_restriction_enzymes.
-
#show_restriction_table ⇒ Object
# === show_restriction_table.
-
#show_reverse_dna_string ⇒ Object
# === show_reverse_dna_string.
-
#show_rna_sequence(i = sequence_object?.to_rna) ⇒ Object
# === show_rna_sequence.
-
#show_save_file ⇒ Object
# === show_save_file ========================================================================= #.
-
#show_segments ⇒ Object
# === show_segments.
-
#show_seq_1(i = seq1?) ) ⇒ Object
# === show_seq_1 ========================================================================= #.
-
#show_seq_2(i = seq2?) ) ⇒ Object
# === show_seq_2 ========================================================================= #.
-
#show_seq_3(i = seq3?) ) ⇒ Object
# === show_seq_3 ========================================================================= #.
-
#show_seq_4 ⇒ Object
# === show_seq_4 ========================================================================= #.
-
#show_seq_5 ⇒ Object
# === show_seq_5 ========================================================================= #.
-
#show_seq_6 ⇒ Object
# === show_seq_6 ========================================================================= #.
-
#show_sequence_in_splitted_form(how_many = 3, use_this_token_for_rejoining = ' ') ⇒ Object
# === show_sequence_in_splitted_form.
-
#show_sequence_with_a_ruler(group_together_n_nucleotides = :default, use_this_sequence = main_sequence?, , type = type? ) ⇒ Object
# === show_sequence_with_a_ruler.
-
#show_sigma_tutorial ⇒ Object
# === show_sigma_tutorial.
-
#show_sixpack_alignment(i = dna_sequence_object? ) ⇒ Object
# === show_sixpack_alignment.
-
#show_start_and_stop_codons ⇒ Object
# === show_start_and_stop_codons.
-
#show_startup_information ⇒ Object
# === show_startup_information.
-
#show_t_phages ⇒ Object
# === show_t_phages ========================================================================= #.
-
#show_taxid(id = 9606) ⇒ Object
# === show_taxid.
-
#show_the_aminoacids_frequencies ⇒ Object
# === show_the_aminoacids_frequencies ========================================================================= #.
-
#show_the_leader? ⇒ Boolean
# === show_the_leader? ========================================================================= #.
-
#show_the_positively_charged_aminoacids ⇒ Object
# === show_the_positively_charged_aminoacids ========================================================================= #.
-
#show_the_trailer? ⇒ Boolean
# === show_the_trailer? ========================================================================= #.
-
#show_the_weight_of_some_common_proteins(use_this_file = FILE_WEIGHT_OF_COMMON_PROTEINS) ⇒ Object
# === show_the_weight_of_some_common_proteins ========================================================================= #.
-
#show_the_weight_of_the_four_individual_nucleotides ⇒ Object
# === show_the_weight_of_the_four_individual_nucleotides ========================================================================= #.
-
#show_this_sequence_padded(i = dna_sequence_object? ) ⇒ Object
# === show_this_sequence_padded.
-
#show_this_subsequence(start_position = 1, end_position = 10, work_on_this_sequence = dna_sequence_object? ) ⇒ Object
# === show_this_subsequence.
-
#show_todo_file ⇒ Object
# === show_todo_file ========================================================================= #.
-
#show_useful_URLs ⇒ Object
# === show_useful_URLs.
-
#show_weight_of_this_nucleotide(i) ⇒ Object
# === show_weight_of_this_nucleotide.
-
#show_welcome_message ⇒ Object
# === show_welcome_message.
-
#show_xorg_buffer ⇒ Object
# === show_xorg_buffer ========================================================================= #.
-
#showorf(i = dna_sequence_object?, , show_how_many_frames = :show_three_frames) ⇒ Object
# === showorf (showorf tag).
-
#shuffle_main_string ⇒ Object
# === shuffle_main_string.
-
#silent_startup? ⇒ Boolean
# === silent_startup? ========================================================================= #.
-
#start_clipboard(i = '"') ⇒ Object
# === start_clipboard.
-
#start_codon? ⇒ Boolean
# === start_codon? ========================================================================= #.
-
#start_gtk_controller ⇒ Object
# === start_gtk_controller ========================================================================= #.
-
#start_search(be_verbose = true) ⇒ Object
# === start_search (start_search tag).
-
#stop_codons? ⇒ Boolean
# === stop_codons? ========================================================================= #.
-
#store_here? ⇒ Boolean
# === store_here?.
-
#three_to_one(i) ⇒ Object
# === three_to_one.
-
#thymin? ⇒ Boolean
# === thymin? ========================================================================= #.
-
#tk_start_three_to_one ⇒ Object
# === start_three_to_one.
-
#to_dna(i = sequence? ) ⇒ Object
# === to_dna ========================================================================= #.
-
#to_fasta(i = dna_sequence? ) ⇒ Object
# === to_fasta.
-
#to_genbank(this_sequence = dna_sequence_as_string? ) ⇒ Object
# === to_genbank.
-
#to_rna(i = seq_object?) ) ⇒ Object
# === to_rna ========================================================================= #.
-
#to_talen(i = dna_sequence? ) ⇒ Object
# === to_talen ========================================================================= #.
-
#toggle_mode ⇒ Object
# === toggle_mode ========================================================================= #.
-
#toggle_truncate ⇒ Object
# === toggle_truncate ========================================================================= #.
-
#toggle_xorg_buffer ⇒ Object
# === toggle_xorg_buffer ========================================================================= #.
-
#trailing_3_prime(get_rid_of_spaces = false) ⇒ Object
(also: #three_trailer, #three_trailer?, #trailer, #three_prime, #trailing_three_prime, #trail_three_prime, #trail_three, #trailing_three)
# === trailing_3_prime.
-
#trailing_five_prime ⇒ Object
(also: #trailing_5_prime, #five_prime_trailer)
# === trailing_five_prime ========================================================================= #.
-
#translate(i, be_verbose = true) ⇒ Object
# === translate.
-
#translate_aminoacid(these_aminoacids = string?, , be_verbose = true) ⇒ Object
# === translate_aminoacid.
-
#translate_dna_into_aminoacid(i = dna_sequence?, , frame = 1) ⇒ Object
(also: #translate_dna_into_aminoacid_frame1)
# === translate_dna_into_aminoacid.
-
#translate_dna_into_aminoacid_frame2(i = nil) ⇒ Object
# === translate_dna_into_aminoacid_frame2 ========================================================================= #.
-
#translate_dna_into_aminoacid_frame3(i = nil) ⇒ Object
# === translate_dna_into_aminoacid_frame3 ========================================================================= #.
-
#try_to_compare_these_two_sequences_for_equality(i) ⇒ Object
# === try_to_compare_these_two_sequences_for_equality.
-
#try_to_display_this_fasta_entry(i) ⇒ Object
# === try_to_display_this_fasta_entry ========================================================================= #.
-
#try_to_find_restriction_enzymes_for(i) ⇒ Object
(also: #find_this_sequence, #find_in_main_sequence)
# === try_to_find_restriction_enzymes_for.
-
#try_to_find_this_restriction_enzyme(i) ⇒ Object
# === try_to_find_this_restriction_enzyme.
-
#try_to_report_the_version_of_bedtools ⇒ Object
# === try_to_report_the_version_of_bedtools ========================================================================= #.
-
#try_to_report_the_version_of_viennarna ⇒ Object
# === try_to_report_the_version_of_viennarna.
-
#try_to_run_rnalfold_on_this_file(i) ⇒ Object
# === try_to_run_rnalfold_on_this_file ========================================================================= #.
-
#try_to_show_the_configuration ⇒ Object
# === try_to_show_the_configuration ========================================================================= #.
-
#type? ⇒ Boolean
# === type? ========================================================================= #.
-
#uncolourize_this_aminoacid(i) ⇒ Object
# === uncolourize_this_aminoacid ========================================================================= #.
-
#unfreeze_the_main_sequence ⇒ Object
# === unfreeze_the_main_sequence ========================================================================= #.
-
#uniprot_fetch(i = 'P12345') ⇒ Object
# === uniprot_fetch.
-
#upcase_main_string ⇒ Object
# === upcase_main_string.
-
#uracil? ⇒ Boolean
# === uracil? ========================================================================= #.
-
#use_expand_cd_aliases? ⇒ Boolean
# === use_expand_cd_aliases? ========================================================================= #.
-
#use_this_fasta_file(at_position = 1) ⇒ Object
# === use_this_fasta_file.
-
#use_which_prompt? ⇒ Boolean
# === use_which_prompt? ========================================================================= #.
-
#use_xsel? ⇒ Boolean
# === use_xsel? ========================================================================= #.
-
#user_input? ⇒ Boolean
# === user_input? ========================================================================= #.
-
#verbose_handle_this_sys_command(i, arguments = a? ) ⇒ Object
# === verbose_handle_this_sys_command ========================================================================= #.
-
#verbose_report_numbered_amino_acid_sequence(i, which_frame = '1') ⇒ Object
# === verbose_report_numbered_amino_acid_sequence.
-
#verbose_save_history_to_file ⇒ Object
# === verbose_save_history_to_file ========================================================================= #.
-
#version? ⇒ Boolean
# === version? ========================================================================= #.
-
#weight_of_adenin? ⇒ Boolean
# === weight_of_adenin? ========================================================================= #.
-
#weight_of_cytosin? ⇒ Boolean
# === weight_of_cytosin? ========================================================================= #.
-
#weight_of_guanin? ⇒ Boolean
# === weight_of_guanin? ========================================================================= #.
-
#weight_of_thymin? ⇒ Boolean
# === weight_of_thymin? ========================================================================= #.
-
#weight_of_uracil? ⇒ Boolean
# === weight_of_uracil? ========================================================================= #.
-
#wget(i) ⇒ Object
# === wget (wget tag).
-
#what_sequence_is_this?(i = dna_sequence? ) ⇒ Boolean
# === what_sequence_is_this?.
-
#will_we_truncate? ⇒ Boolean
# === will_we_truncate? ========================================================================= #.
-
#will_we_use_colours? ⇒ Boolean
# === will_we_use_colours? ========================================================================= #.
-
#www_finder_run ⇒ Object
# === www_finder_run ========================================================================= #.
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$/ # ======================================================================= # # === bioshell --controller # ======================================================================= # when /^-?-?controller$/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$/i require 'bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb' ::Bioroebe::GUI::Gtk::ProteinToDNA. exit # ======================================================================= # # === bioshell --permanently-disable-startup-intro # === bioshell --permanently-disable-startup-notice # === bioshell --permanently-no-startup-intro # === bioshell --permanently-no-startup-info # ======================================================================= # when /^-?-?permanently(-|_)?disable(-|_)?startup(-|_)?intro$/, /^-?-?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.
#
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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
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# File 'lib/bioroebe/shell/shell.rb', line 11840 def self.(i = ARGV) new(:no_commandline_arguments).(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.do_login 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' ) = i.scan(/\d+/).first position = rand(main_sequence?.size)+1 e 'Next adding '+sfancy()+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:
ATGCCC
#
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# File 'lib/bioroebe/shell/shell.rb', line 10957 def ( 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”.
#
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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)
#
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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.
#
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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?
#
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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.
#
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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?
#
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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.
#
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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.('~').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.
#
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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?
#
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# File 'lib/bioroebe/shell/shell.rb', line 7461 def @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?
#
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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
#
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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?
#
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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?
#
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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. # ======================================================================= # # === 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?
#
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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?
#
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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.
#
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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. # ======================================================================= # # === 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 = ( @internal_hash[:command_to_be_passed_to_the_menu] ) case # ============================================================= # # === :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?
#
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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.
#
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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?
#
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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?
#
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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?
#
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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?
#
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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.
#
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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.
#
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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 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?
#
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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?
#
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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?
#
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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?
#
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# File 'lib/bioroebe/shell/shell.rb', line 10867 def is_dna? mode? == :dna end |
#is_palindrome?(i) ⇒ Boolean
#
is_palindrome?
#
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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?
#
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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.
#
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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.
#
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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.
#
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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.
#
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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?
#
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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 ( i = , 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| (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$/, 'icolours' # ===================================================================== # # === aligned # ===================================================================== # when 'aligned', 'aligned?', 'beauty', 'beautified', # We show the DNA sequence correctly aligned. 'formatted', 'padded', 'beaut', 'falign', 'blocked', 'block', /^show(_|-)?this(_|-)?sequence(_|-)?padded$/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') } (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. } 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' # ===================================================================== # # === 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 # ===================================================================== # # === 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$/, 'save' save_my_file { :be_verbose } # ===================================================================== # # === rev? # ===================================================================== # when 'rev?' e 'Testing rev next, the ability to revert to the default colour.' pp ::Bioroebe.rev if ::Bioroebe.rev.empty? e 'Not using any special colours presently.' else e 'Using special colours.' end e "Red then revert, if colours are enabled: "\ "#{swarn('Red then')}#{rev} revert." # ===================================================================== # # === available_colours? # ===================================================================== # when /^available_?colours\??/, /^show_?html_?colours/, 'highlight?' show_html_colours # ===================================================================== # # === seq_with_tab? # ===================================================================== # when /seq_?with_?tab\??/, 'splitted', 'splitter' show_string { :with_colourized_separator } # ===================================================================== # # === barrier # ===================================================================== # when 'barrier','vertical','verti', /^add(_|-)?vertical(_|-)?barrier(_|-)?to(_|-)?sequence$/ (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 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?
#
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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
#
6465 6466 6467 6468 6469 6470 6471 6472 6473 6474 6475 6476 6477 6478 6479 6480 6481 6482 6483 6484 6485 6486 6487 6488 6489 6490 6491 6492 6493 6494 6495 6496 6497 6498 6499 6500 6501 6502 6503 6504 6505 6506 6507 6508 6509 6510 6511 6512 6513 6514 6515 6516 6517 6518 6519 6520 6521 6522 6523 6524 6525 6526 6527 6528 6529 6530 6531 6532 6533 6534 6535 6536 6537 6538 6539 6540 6541 6542 6543 |
# 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?
#
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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?
#
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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.
#
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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?
#
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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.
#
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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.
#
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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?
#
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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.
#
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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
#
perform_a_pubmed_search
#
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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.
#
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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.
#
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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?
#
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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?
#
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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?
#
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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. # ======================================================================= # = " 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')})"+ 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 erev Bioroebe::VerboseTruth[] 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?
#
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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(). # The welcome-message should come after the startup actions. ( 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?
#
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# File 'lib/bioroebe/shell/shell.rb', line 10121 def run_in_GUI_mode? runmode? == :GUI end |
#run_nls_search ⇒ Object
#
run_nls_search
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 ( i = , 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| (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$/, 'icolours' # ===================================================================== # # === aligned # ===================================================================== # when 'aligned', 'aligned?', 'beauty', 'beautified', # We show the DNA sequence correctly aligned. 'formatted', 'padded', 'beaut', 'falign', 'blocked', 'block', /^show(_|-)?this(_|-)?sequence(_|-)?padded$/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') } (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. } 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' # ===================================================================== # # === 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 # ===================================================================== # # === 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$/, 'save' save_my_file { :be_verbose } # ===================================================================== # # === rev? # ===================================================================== # when 'rev?' e 'Testing rev next, the ability to revert to the default colour.' pp ::Bioroebe.rev if ::Bioroebe.rev.empty? e 'Not using any special colours presently.' else e 'Using special colours.' end e "Red then revert, if colours are enabled: "\ "#{swarn('Red then')}#{rev} revert." # ===================================================================== # # === available_colours? # ===================================================================== # when /^available_?colours\??/, /^show_?html_?colours/, 'highlight?' show_html_colours # ===================================================================== # # === seq_with_tab? # ===================================================================== # when /seq_?with_?tab\??/, 'splitted', 'splitter' show_string { :with_colourized_separator } # ===================================================================== # # === barrier # ===================================================================== # when 'barrier','vertical','verti', /^add(_|-)?vertical(_|-)?barrier(_|-)?to(_|-)?sequence$/ (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 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?
#
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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?
#
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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?
#
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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?
#
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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 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
#
show_copyright_clause
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?
#
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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
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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?
#
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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?
#
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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 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?
#
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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?
#
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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?
#
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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.
#
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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?
#
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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() colourized_yes_or_no = simp(_.to_s) erev 'Will we use class Rcfiles::DirectoryAliases: '+ colourized_yes_or_no end |
#type? ⇒ Boolean
#
type?
#
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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?
#
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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?
#
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# File 'lib/bioroebe/shell/shell.rb', line 5668 def ::Bioroebe::Configuration. 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?
#
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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?
#
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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?
#
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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?
#
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# File 'lib/bioroebe/shell/shell.rb', line 8061 def version? ::Bioroebe.version end |
#weight_of_adenin? ⇒ Boolean
#
weight_of_adenin?
#
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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?
#
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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?
#
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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?
#
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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?
#
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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.
#
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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?
#
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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 |