Class: Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb

Overview

Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence

Constant Summary

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from CommandlineApplication

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

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_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 = nil, use_this_codon_table = :default, run_already = true) ⇒ MostLikelyNucleotideSequenceForThisAminoacidSequence

#

initialize

#

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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 33

def initialize(
    commandline_arguments = nil,
    use_this_codon_table  = :default,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    when :be_quiet
      set_be_quiet
    end
  end
  set_use_this_codon_table(use_this_codon_table)
  run if run_already
end

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::MostLikelyNucleotideSequenceForThisAminoacidSequence[]

#

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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 135

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

Instance Method Details

#codon_percenage? ⇒ Boolean

#

codon_percentage?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 89

def codon_percenage?
  @internal_hash[:codon_percentage]
end

#final_sequence? ⇒ Boolean Also known as: sequence?

#

final_sequence?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 128

def final_sequence?
  @internal_hash[:final_sequence]
end

#name_of_the_codon_table? ⇒ Boolean

#

name_of_the_codon_table?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 82

def name_of_the_codon_table?
  @internal_hash[:codon_percentage].name_of_the_codon_table?
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 59

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @internal_hash
  # ======================================================================= #
  @internal_hash = {}
  # ======================================================================= #
  # === :codon_percentage
  # ======================================================================= #
  @internal_hash[:codon_percentage] = Bioroebe::CodonPercentage.new
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 96

def run
  _ = first?.delete('-').split(//)
  erev 'The aminoacid sequence '+steelblue(_.join)+rev+
       ' is best represented by:' if be_verbose?
  codon_percentage = codon_percenage?
  all_codons = ::Bioroebe.possible_codons_for_these_aminoacids(_)
  final_sequence = ''.dup
  all_codons.each {|array_codons|
    max_value = array_codons.map {|this_codon|
      codon_percentage[this_codon]
    }
    # ===================================================================== #
    # Next we build a sorted Hash representing these frequencies:
    # ===================================================================== #
    max_element = array_codons.zip(max_value).
                  max_by {|key, value| value }.first # This will give us: "ATC" from ["ATC", 20.8]
    final_sequence << max_element
  }
  @internal_hash[:final_sequence] = final_sequence
  if be_verbose?
    e
    e "  5'-#{colourize_nucleotide_sequence(final_sequence)}-3'"
    e
    erev 'This assumes the codon table '+
         steelblue(name_of_the_codon_table?)+
         rev+'.'
  end
end

#set_use_this_codon_table(i) ⇒ Object

#

set_use_this_codon_table

#

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# File 'lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb', line 75

def set_use_this_codon_table(i)
  @internal_hash[:codon_percentage].set_use_this_codon_table(i)
end