Class: Bioroebe::Taxonomy::IsDNA
- Inherits:
-
Object
- Object
- Bioroebe::Taxonomy::IsDNA
show all
- Includes:
- Shared
- Defined in:
- lib/bioroebe/taxonomy/info/is_dna.rb
Overview
Constant Summary
Constants included
from Constants
Constants::AA_DIR, Constants::ARRAY_PROJECT_FILES, Constants::Archaea_Taxonomy_ID, Constants::BASE, Constants::BASE_URL, Constants::BE_VERBOSE, Constants::Bacteria_Taxonomy_ID, Constants::CITATIONS, Constants::CURATED_DIR, Constants::DATA_DIR, Constants::DELNODES, Constants::DIVISION, Constants::Eukaryota_Taxonomy_ID, Constants::FILE_USE_THIS_DATABASE, Constants::GEM_DIR, Constants::GENCODE, Constants::INCOMING_DIR, Constants::INFO_DIR, Constants::LAST_INTERACTIVE_COMMAND, Constants::LOCALOME_DIR, Constants::LOCAL_MIRROR, Constants::MERGED, Constants::MODULE_PATH, Constants::NAMES, Constants::NAMES_SQL, Constants::NCBI_BASE, Constants::NODES, Constants::NODES_SQL, Constants::NT_DIR, Constants::POSTGRESQL_QUERY_SIZE, Constants::POSTGRE_LOGIN_COMMAND, Constants::PROJECT_DOC_DIR, Constants::SEQUENCES_DIR, Constants::SHARED_HOME, Constants::TAXONOMY_BROWSER, Constants::TEMP_DIR, Constants::TEST_DIR, Constants::TMP_DIR, Constants::URL1
Instance Attribute Summary collapse
Class Method Summary
collapse
Instance Method Summary
collapse
Methods included from Shared
be_quiet, be_verbose?, #be_verbose?, #cd, #edit_login_file, #eliminate_tabulator, #ensure_that_download_dir_exists, #ensure_that_temp_dir_exists, #mkdir, #readlines, #set_pgpassword, #show_password, #show_time_now, #split_at, #split_at_tabulator, #tokenize
Methods included from Constants
#info_dir?, #work_directory?
Constructor Details
#initialize(i = 'MGMGMGMMM', run_already = true) ⇒ IsDNA
35
36
37
38
39
40
41
42
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 35
def initialize(
i = 'MGMGMGMMM',
run_already = true
)
reset
set_input(i)
run if run_already
end
|
Instance Attribute Details
#n_entries ⇒ Object
30
31
32
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 30
def n_entries
@n_entries
end
|
Class Method Details
.[](i = ARGV) ⇒ Object
#
Class method for a more convenient output.
#
147
148
149
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 147
def self.[](i = ARGV)
return new(i).result
end
|
Instance Method Details
#determine_how_many_characters_we_have ⇒ Object
#
determine_how_many_characters_we_have
#
75
76
77
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 75
def determine_how_many_characters_we_have
@total_characters = @input.join('').size
end
|
#is_dna? ⇒ Boolean
#
is_dna?
Query method to determine whether this is DNA or whether it is not.
#
92
93
94
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 92
def is_dna?
@result
end
|
#report ⇒ Object
#
report
Do a verbose report here.
#
101
102
103
104
105
106
107
108
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 101
def report
is_or_is_not_dna = ''
if is_dna?
else
is_or_is_not_dna << steelblue('not ')
end
erev 'The dataset is '+is_or_is_not_dna+rev+'DNA.'
end
|
#reset ⇒ Object
47
48
49
50
51
52
53
54
55
56
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 47
def reset
@be_verbose = false
@n_entries = 0
end
|
#result? ⇒ Boolean
Also known as:
result
113
114
115
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 113
def result?
@result
end
|
#run ⇒ Object
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 120
def run
result = true
@input.each {|entry|
splitted = entry.chars
splitted.each {|inner_entry|
@n_entries += 1
if ARRAY_VALID_DNA_SEQUENCES.include? inner_entry
else if @be_verbose
e "Nope, #{sfancy(inner_entry)} is not DNA."
pp splitted
end
result = false
break
end
}
}
@result = result
return result
end
|
61
62
63
64
65
66
67
68
69
70
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 61
def set_input(i)
if File.exist? i
if Object.const_defined? Taxonomy::ParseFasta
i = Taxonomy::ParseFasta.new(i)
end
end if i.is_a? String
i = [i].flatten
@input = i
determine_how_many_characters_we_have
end
|
#total_characters? ⇒ Boolean
Also known as:
total_characters
82
83
84
|
# File 'lib/bioroebe/taxonomy/info/is_dna.rb', line 82
def total_characters?
@total_characters
end
|