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, #show_the_weight_of_these_aminoacids?

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, &block) ⇒ Trypsin

#

initialize

#


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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 33

def initialize(
    commandline_arguments = nil,
    run_already           = true,
    &block
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  # ======================================================================= #
  # === Handle blocks given to this method next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :be_quiet
    # ===================================================================== #
    when :be_quiet
      set_be_quiet
    end
  end
  run if run_already
end

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::Trypsin[]

#


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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 224

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

Instance Method Details

#display_the_result_similar_to_pp_output ⇒ Object

#

display_the_result_similar_to_pp_output

#


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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 118

def display_the_result_similar_to_pp_output
  print '['
  @result.each_with_index {|entry, index|
    print entry
    print ', ' unless index == (@result.size - 1)
  }
  print ']'
  e
end

#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 85

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

#report ⇒ Object

#

report (report tag)

#


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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 131

def report
  @internal_hash[: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?
    old_position = 0
    if be_verbose?
      display_the_result_similar_to_pp_output
      erev 'The following peptide fragments would be obtained '\
           'if this were to be cut via Trypsin:'
      e
      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
    end
    @result.each {|this_position|
      this_subsequence = the_sequence[old_position .. (this_position - 1)]
      old_position = this_position
      if be_verbose?
        erev '  after the aminoacid-position '+
             sfancy(this_position.to_s.rjust(3))+
             rev+
             ': '+
             steelblue(
               this_subsequence
             )+crimson('↓')+
             rev
      end
      # =================================================================== #
      # === Show the weight of these aminoacids, if instructed to do so
      # =================================================================== #
      weight_of_this_peptide_fragment = Bioroebe.weight_of_this_aminoacid?(
        this_subsequence.split(//)
      ).round(5)
      @internal_hash[:array_peptide_fragments] << [
        this_subsequence, weight_of_this_peptide_fragment
      ]
      if show_the_weight_of_these_aminoacids? and be_verbose?
        erev ''.ljust(36)+'Weight of this peptide fragment: '+
             olivedrab(weight_of_this_peptide_fragment.to_s)
      end
    }
    if be_verbose?
      e
      unless @internal_hash[:array_peptide_fragments].empty?
        show_sorted_peptide_fragments(@internal_hash[:array_peptide_fragments])
      end
    end
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 61

def reset
  super()
  set_be_verbose
  # ======================================================================= #
  # === @array_cut_at_these_aminoacids
  #
  # This variable ensures that trypsine cuts after lysines (K) and
  # arginines (R).
  # ======================================================================= #
  @array_cut_at_these_aminoacids = %w( K R )
  # ======================================================================= #
  # === :array_peptide_fragments
  #
  # This class will store the peptide fragments into this unsorted
  # Array.
  # ======================================================================= #
  @internal_hash[:array_peptide_fragments] = []
end

#result? ⇒ Boolean

#

result?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 111

def result?
  @result
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 215

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 = ) ⇒ Object

#

show_sorted_peptide_fragments

#


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# File 'lib/bioroebe/cleave_and_digest/trypsin.rb', line 195

def show_sorted_peptide_fragments(
    i = @internal_hash[:array_peptide_fragments]
  )
  sorted = i.sort_by {|fragment, weight| weight}.reverse
  erev 'Next, the '+steelblue('five heaviest fragments')+
       rev+' 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