Class: Bioroebe::FindGene

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

Overview

Bioroebe::FindGene

Constant Summary collapse

DEFAULT_STRING =
#

DEFAULT_STRING

#
'AUGGGAUAUUGUGUGUAUGGGAGGAGAGAUGAAUAGUAGUUAGUUUAUAGAAA'

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, #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(i = nil, run_already = true) ⇒ FindGene

#

initialize

#

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 34

def initialize(
    i           = nil,
    run_already = true
  )
  reset
  set_input(i)
  run if run_already
end

Class Method Details

.[](i) ⇒ Object

#

Bioroebe::FindGene[]

#

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 194

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

Instance Method Details

#check_whether_we_have_dna_as_input ⇒ Object

#

check_whether_we_have_dna_as_input

#

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 175

def check_whether_we_have_dna_as_input
  if @input.include? 'U'
    @input = @input.dup if @input.frozen?
    @input.tr!('U','T')
  end
end

#did_not_find_any_gene ⇒ Object

#

did_not_find_any_gene

#

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 138

def did_not_find_any_gene
  erev 'We did not find any gene in the input sequence `'+
        sfancy(@input)+
        rev+'`.'
  erev 'We did use the following elements:'
  e
  erev "  Start codon: #{simp(start_codon?)}"
  erev '  Stop  codon: '+simp(stop_codons?.join(','))
  e
end

#input? ⇒ Boolean

#

input?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 87

def input?
  @input
end

#process_string ⇒ Object

#

process_string

#

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 94

def process_string
  0.step(@input.size, 3) { |current_position|
    _ = @input[current_position, 3]
    if _ == start_codon? # Match to the given start-codon.
      # e 'We found a Start Codon.'
      @start_codon_positions << current_position
    end
    if stop_codons?.include? _
      # e 'We found a Stop Codon.'
      @stop_codon_positions << current_position
    end
  }
end

#report_gene ⇒ Object

#

report_gene

We try to report whether we have found a gene.

#

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 154

def report_gene
  unless @start_codon_positions.empty?
    unless @stop_codon_positions.empty?
      start = @start_codon_positions[0]
      end_position = @stop_codon_positions[0]
      erev 'Found `'+simp(@input[start, end_position])+rev+'` in '\
           'the string'
      erev sfancy(input?)+rev+','
      erev 'which should include the '\
           'start codon ('+start_codon?.to_s+rev+').'
    else
      did_not_find_any_gene
    end
  else
    did_not_find_any_gene
  end
end

#reset ⇒ Object

#

reset

#

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 46

def reset
  super()
  # ======================================================================= #
  # === @start_codon_positions
  # ======================================================================= #
  @start_codon_positions = [] # This will contain the start codons.
  # ======================================================================= #
  # === @stop_codon_positions
  # ======================================================================= #
  @stop_codon_positions  = []
  if stop_codons?.empty?
    # ===================================================================== #
    # Determine the stop-codons in this case.
    # ===================================================================== #
    ::Bioroebe.determine_the_stop_codons
  end
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 185

def run
  check_whether_we_have_dna_as_input # Must check if we have RNA or DNA as input.
  process_string
  report_gene
end

#set_input(i = '') ⇒ Object

#

set_input

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 77

def set_input(i = '')
  i = i.first if i.is_a? Array
  i = i.dup if i
  i = DEFAULT_STRING if i.nil?
  @input = i
end

#start_codon? ⇒ Boolean Also known as: start_codons?

#

start_codon?

Only give back the first instance of any start codon found.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 131

def start_codon?
  ::Bioroebe.start_codon?
end

#start_stop? ⇒ Boolean

#

start_stop?

Return an Array with the start and stop codon position.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 122

def start_stop?
  [ start_codon?, stop_codon? ]
end

#stop_codon? ⇒ Boolean

#

stop_codon?

Only give back the first instance of any stop codon found.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 113

def stop_codon?
  @stop_codon_positions.first
end

#stop_codons? ⇒ Boolean

#

stop_codons?

This getter-method will return which stop-codons exist for the given organism at hand.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/utility_scripts/find_gene.rb', line 70

def stop_codons?
  ::Bioroebe.stop_codons?
end