Class: Bioroebe::ConsensusSequence

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

Overview

Bioroebe::ConsensusSequence

Constant Summary collapse

A_T_or_C =
#

A_T_or_C

#
%w( A T C )

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

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(*i) ⇒ ConsensusSequence

#

initialize

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 29

def initialize(*i)
  reset
  run_already = true # This is the default value.
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded # case tag
    # ===================================================================== #
    # === :do_not_run_yet_and_be_quiet
    # ===================================================================== #
    when :do_not_run_yet_and_be_quiet
      run_already = false
      set_be_quiet
      @report_the_frequencies = false
    # ===================================================================== #
    # === :do_not_run_yet
    # ===================================================================== #
    when :do_not_run_yet
      run_already = false
    # ===================================================================== #
    # === :be_quiet
    # ===================================================================== #
    when :be_quiet
      set_be_quiet
      @report_the_frequencies = false
    end
  end
  set_input_sequences(i)
  run if run_already
end

Instance Method Details

#calculate_frequencies_of(array) ⇒ Object

#

calculate_frequencies_of

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 191

def calculate_frequencies_of(array)
  hash = {}
  hash['A'] = array.count('A')
  hash['T'] = array.count('T')
  hash['C'] = array.count('C')
  hash['G'] = array.count('G')
  return hash
end

#colourize_nucleotide_position(i) ⇒ Object

#

colourize_nucleotide_position

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 142

def colourize_nucleotide_position(i)
  seagreen(i)
end

#consensus_sequence? ⇒ Boolean

#

consensus_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 184

def consensus_sequence?
  @array_consensus_positions.join
end

#display_an_even_simpler_consensus_sequence(i = consensus_sequence? ) ⇒ Object

#

display_an_even_simpler_consensus_sequence

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 264

def display_an_even_simpler_consensus_sequence(
    i = consensus_sequence?
  )
  this_sequence = orange(return_an_even_simpler_consensus_sequence(i))
  erev "  #{this_sequence}#{rev} "\
       "# ← a very likely consensus sequence"
end

#input_sequences? ⇒ Boolean

#

input_sequences?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 84

def input_sequences?
  @input_sequences
end

#iterate_over_the_sequences ⇒ Object Also known as: determine_the_consensus_sequences

#

iterate_over_the_sequences

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 98

def iterate_over_the_sequences
  size = @input_sequences.first.size
  0.upto(size - 1) {|n|
    mapped = @input_sequences.map {|line| line[n,1] }
    frequencies = calculate_frequencies_of(mapped)
    # ===================================================================== #
    # max_value has two values:
    #
    #   (1) the nucleotide
    #   (2) the amount of times that nucleotide occurs
    #
    # We can not use .max_by because it returns only one result; so we
    # have to use .group_by instead.
    # ===================================================================== #
    # max_value = frequencies.max_by {|key, value| value }
    max_value = frequencies.group_by {|key, value| value }.max.last # => [2, 5]
    _ = max_value.map {|first, last| first }
    if _.size > 1
      append_this = '['+_.join('/')+']'
    else
      append_this = _.join
    end
    if @report_the_frequencies
      erev "The #{mediumslateblue('frequencies')}#{rev} "\
           "for #{lightgreen(mapped.join)}#{rev} "+
           '(at '+colourize_nucleotide_position("nucleotide position #{n+1}")+
           rev+') were:'
      e
      print '  '; pp frequencies
      erev "\nThe associated max-value for "+
           colourize_nucleotide_position("nucleotide position #{n+1}")+
           "#{rev} was: "+
           simp(
             max_value.map {|a| a.join(': ') }.join('; ')
           )
      e
    end
    @array_consensus_positions << append_this
  }
end

#random_nucleotide_for_this_IUPAC_code(i) ⇒ Object

#

random_nucleotide_for_this_IUPAC_code

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 149

def random_nucleotide_for_this_IUPAC_code(i)
  case i
  when 'H'
    return_A_or_T_or_C
  when 'M'
    return_A_or_C
  end
end

#report_on_which_sequences_we_will_operate(be_verbose = be_verbose? ) ⇒ Object

#

report_on_which_sequences_we_will_operate

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 203

def report_on_which_sequences_we_will_operate(
    be_verbose = be_verbose?
  )
  case be_verbose
  # ======================================================================= #
  # === :be_verbose
  # ======================================================================= #
  when :be_verbose
    be_verbose = true
  end
  if be_verbose
    e
    erev "#{rev}Working on the following "\
         "#{steelblue(@input_sequences.size)} "\
         "#{rev}sequences next:"
    e
    @input_sequences.each_with_index {|this_sequence, index| index += 1
      e "  #{sfancy(this_sequence)} #{steelblue(index.to_s.rjust(3))}"
    }; e
  end
end

#report_the_consensus_sequence ⇒ Object

#

report_the_consensus_sequence

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 228

def report_the_consensus_sequence
  if be_verbose?
    the_consensus_sequence = consensus_sequence?
    erev 'The consensus sequence is: '
    e
    e "  #{simp(the_consensus_sequence)}"
    e
    if the_consensus_sequence.include? '/'
      # =================================================================== #
      # In this case, we can perhaps simplify it via the IUPAC code.
      # =================================================================== #
      try_to_find_and_report_a_simpler_consensus_sequence(
        the_consensus_sequence
      )
      # =================================================================== #
      # And this here will just pick any even simpler consensus
      # sequence. We assume that this would imply equal likelihood
      # for a given sequence.
      # =================================================================== #
      try_to_find_and_report_an_even_simpler_consensus_sequence(
        the_consensus_sequence
      )
      if be_verbose?
        erev 'Finally, we will display the above findings in a'
        erev 'shorter variant:'
        report_on_which_sequences_we_will_operate
        display_an_even_simpler_consensus_sequence
        e
      end
    end
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 65

def reset
  super()
  # ======================================================================= #
  # === @array_consensus_positions
  # ======================================================================= #
  @array_consensus_positions = []
  # ======================================================================= #
  # === @be_verbose
  # ======================================================================= #
  set_be_verbose
  # ======================================================================= #
  # === @report_the_frequencies
  # ======================================================================= #
  @report_the_frequencies = true
end

#return_A_or_C ⇒ Object

#

return_A_or_C

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 161

def return_A_or_C
  %w( A C ).sample
end

#return_A_or_T ⇒ Object

#

return_A_or_T

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 168

def return_A_or_T
  %w( A T ).sample
end

#return_A_or_T_or_C ⇒ Object

#

return_A_or_T_or_C

This method will randomly pick either A, T or C.

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 177

def return_A_or_T_or_C
  A_T_or_C.sample
end

#return_an_even_simpler_consensus_sequence(i = consensus_sequence? ) ⇒ Object

#

return_an_even_simpler_consensus_sequence

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 275

def return_an_even_simpler_consensus_sequence(
    i = consensus_sequence?
  )
  _ = i.dup
  if _.include? '[A/T/C]'
    _.gsub!(/\[A\/T\/C\]/,
      steelblue(return_A_or_T_or_C)+
      remove_escape_sequence(orange)
    )
  end
  if _.include? '[A/C]'
    _.gsub!(/\[A\/C\]/,
      steelblue(return_A_or_C)+
      remove_escape_sequence(orange)
    )
  end
  if _.include? '[A/T]'
    _.gsub!(/\[A\/T\]/,
      steelblue(return_A_or_T)+
      remove_escape_sequence(orange)
    )
  end
  _
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 355

def run
  report_on_which_sequences_we_will_operate
  iterate_over_the_sequences
  report_the_consensus_sequence
end

#set_input_sequences(i) ⇒ Object

#

set_input_sequences(i)

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 91

def set_input_sequences(i)
  @input_sequences = [i].flatten
end

#try_to_find_and_report_a_simpler_consensus_sequence(i = consensus_sequence? ) ⇒ Object

#

try_to_find_and_report_a_simpler_consensus_sequence

For a list of IUPAC codes there, you can use this link:

https://www.bioinformatics.org/sms/iupac.html
#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 323

def try_to_find_and_report_a_simpler_consensus_sequence(
    i = consensus_sequence?
  )
  erev "#{rev}We will try to find - and report - a simpler consensus sequence:"
  i = orange(i)
  i = i.dup if i.frozen?
  # ======================================================================= #
  # === Handle [A/T/C]
  # ======================================================================= #
  if i.include? '[A/T/C]'
    i.gsub!(/\[A\/T\/C\]/,
      steelblue('H')+
      remove_escape_sequence(orange)
    )
  end
  # ======================================================================= #
  # === Handle [A/C]
  # ======================================================================= #
  if i.include? '[A/C]'
    i.gsub!(/\[A\/C\]/,
      steelblue('M')+
      remove_escape_sequence(orange)
    )
  end
  e
  erev "  #{i}"
  e
end

#try_to_find_and_report_an_even_simpler_consensus_sequence(i = consensus_sequence? ) ⇒ Object

#

try_to_find_and_report_an_even_simpler_consensus_sequence

#


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# File 'lib/bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb', line 303

def try_to_find_and_report_an_even_simpler_consensus_sequence(
    i = consensus_sequence?
  )
  erev "#{rev}And the following is an even simpler consensus "\
       "sequence (blue"
  erev "denotes random, equal choice):"
  _ = return_an_even_simpler_consensus_sequence(i)
  e
  erev "  #{_}"
  e
end