Class: Bioroebe::Genome

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

Overview

Bioroebe::Genome

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, #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 = nil, run_already = true) ⇒ Genome

#

initialize

#


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# File 'lib/bioroebe/genome/genome.rb', line 27

def initialize(
    commandline_arguments = nil,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::Genome[]

#


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# File 'lib/bioroebe/genome/genome.rb', line 122

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

Instance Method Details

#add_the_lac_operon ⇒ Object

#

add_the_lac_operon

If glucose is present and lactose is absent then no transcription of the lac operon occurs.

#


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# File 'lib/bioroebe/genome/genome.rb', line 56

def add_the_lac_operon
  @internal_hash[:lac_operon] = true
end

#all_genes? ⇒ Boolean

#

all_genes?

This method will return all genes.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/genome/genome.rb', line 99

def all_genes?
  result = []
  _ = @internal_hash[:full_sequence]
  @internal_hash[:CDS].map {|start_nucleotide, end_nucleotide|
    result << _[start_nucleotide - 1, (end_nucleotide - start_nucleotide) + 1]
  }
  return result
end

#annotate(array) ⇒ Object

#

annotate

Annotate some genes here, or rather CDS.

#


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# File 'lib/bioroebe/genome/genome.rb', line 113

def annotate(array)
  array.each {|this_array|
    @internal_hash[:CDS] << [this_array.first, this_array.last]
  }
end

#is_the_lac_operon_transcribable? ⇒ Boolean

#

is_the_lac_operon_transcribable?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/genome/genome.rb', line 63

def is_the_lac_operon_transcribable?
  if !lactose_is_present?
    return false
  elsif glucose_is_present? and lactose_is_present?
    return false
  elsif glucose_is_present?
    return true
  else
    return false
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/genome/genome.rb', line 41

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # All CDS shall be denoted here.
  # ======================================================================= #
  @internal_hash[:CDS] = []
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/genome/genome.rb', line 78

def run
  # add_the_lac_operon
  first = first?
  if first and File.exist?(first)
    _ = Bioroebe.parse_fasta(first)
    @internal_hash[:full_sequence] = _.sequence?
    annotate(
      [
        [2931, 3917]
      ]
    ) # This is for the phage.
pp self
pp all_genes?
  end
end