Class: Bioroebe::CodonPercentage
Overview
Bioroebe::CodonPercentage
Constant Summary
Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE
Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Constants inherited
from Base
Base::NAMESPACE
Class Method Summary
collapse
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.[](i = ARGV) ⇒ Object
# === Bioroebe::CodonPercentage[] ========================================================================= #.
Instance Method Summary
collapse
#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codon_to_aminoacid, #codons_for?, #colourize_this_dna_sequence, #complement, #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?, #leading_five_prime, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opne, #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, #set_be_verbose, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into
#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #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
#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_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?, #file_readlines, #infer_the_namespace, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #rds, #register_sigint, #return_pwd, #return_the_first_line_of_this_file, #word_wrap, #write_what_into
Constructor Details
#initialize(commandline_arguments = ARGV, run_already = true) ⇒ CodonPercentage
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 27
def initialize(
commandline_arguments = ARGV,
run_already = true
)
reset
set_commandline_arguments(
commandline_arguments
)
run if run_already
end
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Class Method Details
.[](i = ARGV) ⇒ Object
#
Bioroebe::CodonPercentage[]
#
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 173
def self.[](i = ARGV)
new(i)
end
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Instance Method Details
#[](this_codon) ⇒ Object
#
[]
This method was added primarily to make this class respond similar to a regular Hash in ruby.
#
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 60
def [](this_codon)
this_codon = this_codon.to_s.tr('T','U')
@internal_hash[:dataset][this_codon]
end
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#codon_table? ⇒ Boolean
Also known as:
use_this_codon_table?
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 141
def codon_table?
@internal_hash[:use_this_codon_table]
end
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#dataset? ⇒ Boolean
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 155
def dataset?
@internal_hash[:dataset]
end
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#name_of_the_codon_table? ⇒ Boolean
#
name_of_the_codon_table?
#
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 148
def name_of_the_codon_table?
File.basename(codon_table?)
end
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#reset ⇒ Object
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 41
def reset
super()
infer_the_namespace
@internal_hash = {}
@internal_hash[:dataset] = nil
end
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#run ⇒ Object
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 162
def run
try_to_load_this_codon_frequency(:human)
end
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#set_use_this_codon_table(i) ⇒ Object
#
set_use_this_codon_table
#
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 134
def set_use_this_codon_table(i)
@internal_hash[:use_this_codon_table] = i
end
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#try_to_load_this_codon_frequency(i = '9606_Homo_sapiens.yml') ⇒ Object
#
try_to_load_this_codon_frequency
#
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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 68
def try_to_load_this_codon_frequency(
i = '9606_Homo_sapiens.yml'
)
case i when :homo_sapiens,
:humans,
:human,
:default,
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i = ::Bioroebe::CodonTablesFrequencies::FILE_HOMO_SAPIENS
when :ecoli,
:e_coli,
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i = ::Bioroebe::CodonTablesFrequencies::FILE_E_COLI
when :yeast,
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i = ::Bioroebe::CodonTablesFrequencies::FILE_SACCHAROMYCES_CEREVISIAE
when :cat,
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i = ::Bioroebe::CodonTablesFrequencies::FILE_FELIS_CATUS
when :arabidopsis
i = ::Bioroebe::CodonTablesFrequencies::FILE_ARABIDOPSIS_THALIANA
when :drosophila,
:the_fly,
:fly
i = ::Bioroebe::CodonTablesFrequencies::FILE_DROSOPHILA_MELANOGASTER
end
set_use_this_codon_table(Bioroebe.directory_frequencies?+File.basename(i))
if File.exist? @internal_hash[:use_this_codon_table]
@internal_hash[:dataset] = YAML.load_file(@internal_hash[:use_this_codon_table])
else
no_file_exists_at(file)
end
end
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