Class: Bioroebe::Trypsin

Inherits:
Digestion show all
Defined in:
lib/bioroebe/cleave_and_digest/trypsin.rb

Overview

Bioroebe::Trypsin

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 Digestion

#consider_reading_from_a_file_if_given_as_input_argument_to_this_class, #mediumturquoise_1_to_10, #return_1_to_10, #sequence?, #set_first

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, run_already = true) ⇒ Trypsin

#

initialize

#

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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 28

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

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::Trypsin[]

#

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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 184

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

Instance Method Details

#perform_the_digestion(array_cut_at_these_aminoacids = @array_cut_at_these_aminoacids) ⇒ Object

#

perform_the_digestion

This method will perform the digestion.

#

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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 62

def perform_the_digestion(
    array_cut_at_these_aminoacids = @array_cut_at_these_aminoacids
  )
  # ======================================================================= #
  # Trypsin splits at K and R, so we split on that.
  # ======================================================================= #
  _ = first?.dup.split(//)
  positions = []
  array_cut_at_these_aminoacids.each {|entry|
    positions <<
      _.each_index.select {|inner_entry| _[inner_entry] == entry }
  }
  positions.flatten!
  positions.sort!
  # ======================================================================= #
  # Because ruby arrays begin at 0, whereas peptides are counted from
  # 1, we have to add +1 to each member.
  # ======================================================================= #
  positions.map! {|entry| entry + 1 }
  @result = positions
end

#reportObject

#

report

#

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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 94

def report
  @array_peptide_fragments.clear
  if @result.empty?
    erev 'No cut-sequence was found for Trypsin. (Make sure to '\
         'input an aminoacid sequence.)'
  else
    the_sequence = first?
    print '['; @result.each_with_index {|entry, index|
      print entry
      print ', ' unless index == (@result.size - 1)
    }; print ']'; e
    erev 'The following peptide fragments would be obtained '\
         'if this were to be cut via Trypsin:'
    e
    old_position = 0
    erev ''.ljust(36)+the_sequence
    e ''.ljust(36)+
      colourize_this_aminoacid_sequence_for_the_commandline(
        the_sequence
      )
    e ''.ljust(36)+
      mediumturquoise_1_to_10+
      mediumturquoise_1_to_10+
      mediumturquoise_1_to_10+
      mediumturquoise_1_to_10+
      mediumturquoise_1_to_10

    @result.each {|this_position|
      this_subsequence = the_sequence[old_position .. (this_position - 1)]
      old_position = this_position
      erev '  after the aminoacid-position '+
           sfancy(this_position.to_s.rjust(3))+
           rev+
           ': '+
           steelblue(
             this_subsequence
           )+crimson('')+
           rev
      # =================================================================== #
      # === Show the weight of these aminoacids, if instructed to do so
      # =================================================================== #
      if @show_the_weight_of_these_aminoacids
        weight_of_this_peptide_fragment = Bioroebe.weight_of_this_aminoacid?(
          this_subsequence.split(//)
        ).round(5)
        @array_peptide_fragments << [
          this_subsequence, weight_of_this_peptide_fragment
        ]
        erev ''.ljust(36)+'Weight of this peptide fragment: '+
             olivedrab(weight_of_this_peptide_fragment.to_s)
      end  
    }
    e
    unless @array_peptide_fragments.empty?
      show_sorted_peptide_fragments(@array_peptide_fragments)
    end
  end
end

#resetObject

#

reset (reset tag)

#

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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 42

def reset
  super()
  # ======================================================================= #
  # === @array_cut_at_these_aminoacids
  # ======================================================================= #
  @array_cut_at_these_aminoacids = %w( K R )
  # ======================================================================= #
  # === @array_peptide_fragments
  #
  # This class will store the peptide fragments into this unsorted
  # Array.
  # ======================================================================= #
  @array_peptide_fragments = []
end

#result?Boolean

#

result?

#

Returns:

  • (Boolean)

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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 87

def result?
  @result
end

#runObject

#

run (run tag)

#

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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 175

def run
  consider_reading_from_a_file_if_given_as_input_argument_to_this_class
  perform_the_digestion
  report
end

#show_sorted_peptide_fragments(i = @array_peptide_fragments) ⇒ Object

#

show_sorted_peptide_fragments

#

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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 156

def show_sorted_peptide_fragments(
    i = @array_peptide_fragments
  )
  sorted = i.sort_by {|fragment, weight| weight}.reverse
  erev 'Next, the five heaviest fragments will be shown:'
  e
  # ======================================================================= #
  # Only the top 5 heaviest fragments will be shown:
  # ======================================================================= #
  sorted[0 .. 4].each {|fragment, weight|
    weight = '%.5f' % weight.to_f
    erev weight.to_s.rjust(20)+'   '+
         steelblue(fragment)
  }
end