Class: Bioroebe::CodonPercentage

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/aminoacids/codon_percentage.rb

Overview

Bioroebe::CodonPercentage

Constant Summary

Constants inherited from CommandlineApplication

Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from CommandlineApplication

#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #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, #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, #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

Methods included from BaseModule

#absolute_path, #default_file_read, #file_readlines

Methods included from CommandlineArguments

#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

Methods included from ColoursForBase

#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_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?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #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

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) ⇒ CodonPercentage

#

initialize

#


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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

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::CodonPercentage[]

#


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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 180

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

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 56

def [](this_codon)
  this_codon = this_codon.to_s.tr('T','U')
  @internal_hash[:dataset][this_codon]
end

#codon_table? ⇒ Boolean Also known as: use_this_codon_table?

#

codon_table?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 146

def codon_table?
  @internal_hash[:use_this_codon_table]
end

#dataset? ⇒ Boolean

#

dataset?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 162

def dataset?
  @internal_hash[:dataset]
end

#name_of_the_codon_table?(i = codon_table? ) ⇒ Boolean

#

name_of_the_codon_table?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 153

def name_of_the_codon_table?(
    i = codon_table?
  )
  File.basename(i)
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 41

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === :dataset
  # ======================================================================= #
  @internal_hash[:dataset] = nil
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 169

def run
  # ======================================================================= #
  # The :human variant is the default codon table to use.
  # ======================================================================= #
  try_to_load_this_codon_frequency(:human)
  # try_to_load_this_codon_frequency(:drosophila) # <- This here could be used for testing.
end

#set_use_this_codon_table(i) ⇒ Object

#

set_use_this_codon_table

#


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# File 'lib/bioroebe/aminoacids/codon_percentage.rb', line 132

def set_use_this_codon_table(i)
  case i
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    i = ::Bioroebe::CodonTablesFrequencies::FILE_HOMO_SAPIENS
  end
  @internal_hash[:use_this_codon_table] = i
end

#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 64

def try_to_load_this_codon_frequency(
    i = '9606_Homo_sapiens.yml'
  )
  case i # case tag
  # ======================================================================= #
  # === :homo_sapiens
  #
  # This is the default codon-frequency table.
  # ======================================================================= #
  when :homo_sapiens,
       :humans,
       :human,
       :default,
       1
    i = ::Bioroebe::CodonTablesFrequencies::FILE_HOMO_SAPIENS
  # ======================================================================= #
  # === :ecoli
  # ======================================================================= #
  when :ecoli,
       :e_coli,
       2
    i = ::Bioroebe::CodonTablesFrequencies::FILE_E_COLI
  # ======================================================================= #
  # === :yeast
  # ======================================================================= #
  when :yeast,
       3
    i = ::Bioroebe::CodonTablesFrequencies::FILE_SACCHAROMYCES_CEREVISIAE
  # ======================================================================= #
  # === :cat
  #
  # This entry point is for the domestic cat.
  # ======================================================================= #
  when :cat,
       4
    i = ::Bioroebe::CodonTablesFrequencies::FILE_FELIS_CATUS
  # ======================================================================= #
  # === :arabidopsis
  #
  # This entry point is for Arabidopsis thaliana.
  # ======================================================================= #
  when :arabidopsis
    i = ::Bioroebe::CodonTablesFrequencies::FILE_ARABIDOPSIS_THALIANA
  # ======================================================================= #
  # === :drosophila
  #
  # This entry point is for the fruit fly.
  # ======================================================================= #
  when :drosophila,
       :the_fly,
       :fly
    i = ::Bioroebe::CodonTablesFrequencies::FILE_DROSOPHILA_MELANOGASTER
  # else
  # else use the number ID.
  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