Class: Bioroebe::Levensthein

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

Overview

Bioroebe::Levensthein

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
DEFAULT_MATCH_COST =
#

DEFAULT_MATCH_COST

The default cost for a match between two nucleotide sequences.

#
10
DEFAULT_MISMATCH_COST =
#

DEFAULT_MISMATCH_COST

The default cost for a mismatch between two nucleotide sequences.

#
-3
DEFAULT_GAP_COST =
#

DEFAULT_GAP_COST

The default cost for a gap between two nucleotide sequences.

#
-1
DEFAULT_STRING1 =
#

DEFAULT_STRING1

#
'CGTCAGCGTACTT'
DEFAULT_STRING2 =
#

DEFAULT_STRING2

#
'ATTC--CGTACTT'

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

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, #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(string1 = nil, string2 = nil, run_already = true) ⇒ Levensthein

#

initialize

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 65

def initialize(
    string1     = nil, # The first sequence.
    string2     = nil, # The second sequence.
    run_already = true
  )
  reset # reset() must come very early.
  register_sigint
  case string1
  when :dont_run_yet
    string1 = nil
    run_already = false
  end
  parse_string1_and_string2(string1, string2) # Must come after the ^^^ above check.
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :be_quiet
    # ===================================================================== #
    when :be_quiet
      @be_verbose = false
    end
  end
  run if run_already
end

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::Levensthein[]

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 685

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

Instance Method Details

#ask_the_user_to_assign_different_scores ⇒ Object

#

ask_the_user_to_assign_different_scores (user input)

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 378

def ask_the_user_to_assign_different_scores
  erev 'Input new scores next, for:'
  print '  match_cost: '
  new_match_cost = $stdin.gets.chomp.to_i
  set_match_cost(new_match_cost)
  erev 'The new match_cost will be '+sfancy(@match_cost)+rev+'.'
  print '  mismatch_cost: '
  new_mismatch_cost = $stdin.gets.chomp.to_i
  set_mismatch_cost(new_mismatch_cost)
  erev 'The new mismatch_cost will be '+sfancy(@mismatch_cost)+rev+'.'
  print '  gap_cost: '
  new_gap_cost = $stdin.gets.chomp.to_i
  set_gap_cost(new_gap_cost)
end

#calculate_the_amount_of_mismatches_and_gaps ⇒ Object

#

calculate_the_amount_of_mismatches_and_gaps

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 613

def calculate_the_amount_of_mismatches_and_gaps
  the_string1 = string1?
  the_string2 = string2?
  process_these_characters = the_string1.chars
  process_these_characters.each_with_index {|character, index|
    target_character = the_string2[index]
    if character == target_character
      # =================================================================== #
      # This must be a match then.
      # =================================================================== #
      increment_n_matches_by(1)
    else
      # =================================================================== #
      # else it is a mismatch UNLESS the target character is '-'.
      # in which case it must be a gap.
      # =================================================================== #
      if (character == '-') or (target_character == '-')
        increment_n_gaps_by(1)
      else
        increment_n_mismatches_by(1)
      end
    end
  }
end

#calculate_the_total_cost ⇒ Object Also known as: total_score?

#

calculate_the_total_cost

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 585

def calculate_the_total_cost
  (match_cost?    * n_matches?) +
  (mismatch_cost? * n_mismatches?) +
  (gap_cost?      * n_gaps?)
end

#determine_the_edit_distance(string1 = string1? ) ⇒ Object

#

determine_the_edit_distance

This method will determine the edit distance between our two inputted Strings.

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 303

def determine_the_edit_distance(
    string1 = string1?
  )
  @internal_hash[:edit_distance] = ::Bioroebe.calculate_levensthein_distance(
    string1,
    string2?,
    :be_quiet
  )
end

#do_report ⇒ Object Also known as: report

#

do_report (report tag)

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 569

def do_report
  report_the_edit_distance
  report_the_amount_of_mismatches_and_gaps
  report_the_total_cost
  erev 'Showing the alignment, with index-positions on top: '\
       '(0 means 10 or 20 or 30 etc)'
  e
  show_numbered_header
  show_first_string
  show_second_string
  e
end

#edit_distance? ⇒ Boolean

#

edit_distance?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 316

def edit_distance?
  @internal_hash[:edit_distance]
end

#gap_cost? ⇒ Boolean Also known as: score_for_gap?, score_for_gaps?, score_for_gaps

#

gap_cost?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 263

def gap_cost?
  @internal_hash[:gap_cost]
end

#increment_n_gaps_by(i = 1) ⇒ Object

#

increment_n_gaps_by

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 505

def increment_n_gaps_by(i = 1)
  @internal_hash[:n_gaps] += i
end

#increment_n_matches_by(i = 1) ⇒ Object

#

increment_n_matches_by

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 512

def increment_n_matches_by(i = 1)
  @internal_hash[:n_matches] += i
end

#increment_n_mismatches_by(i = 1) ⇒ Object

#

increment_n_mismatches_by

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 498

def increment_n_mismatches_by(i = 1)
  @internal_hash[:n_mismatches] += i
end

#initial_padding_to_use? ⇒ Boolean

#

initial_padding_to_use?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 148

def initial_padding_to_use?
  @internal_hash[:initial_padding_to_use]
end

#match_cost? ⇒ Boolean Also known as: score_for_match?

#

match_cost?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 293

def match_cost?
  @internal_hash[:match_cost]
end

#menu(i) ⇒ Object

#

menu (menu tag)

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 396

def menu(i)
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === levensthein --costs
    # ===================================================================== #
    when /^-?-?costs/i,
         /^-?-?use(-|_)?different(-|_)?costs/i,
         /^-?-?input(-|_)?costs/i
      ask_the_user_to_assign_different_scores
    # ===================================================================== #
    # === levensthein --read_sequences_from_this_file=/Depot/j/foo2.md
    # ===================================================================== #
    when /-?-?read(-|_)?sequences(-|_)?from(-|_)?this(-|_)?file=(.+)/
      _ = $5.to_s.dup
      try_to_read_sequences_from_this_file(_)
    # ===================================================================== #
    # === levensthein --use-this-file=/Depot/j/foo.md
    # ===================================================================== #
    when /-?-?use(-|_)?this(-|_)?file=(.+)/
      _ = $3.to_s.dup
      try_to_use_this_file_as_input(_)
    # ===================================================================== #
    # === levensthein --help
    # ===================================================================== #
    when /^-?-?help$/i
      show_help
      exit
    # ===================================================================== #
    # === levensthein --start-gui
    # ===================================================================== #
    when /-?-?start(-|_)?gui$/i,
         /-?-?gui$/i # leven --GUI
      disable_warnings
      require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
      enable_warnings
      ::Bioroebe::GUI::Gtk::LevenstheinDistance.start_gui_application
    # ===================================================================== #
    # === levensthein ATG ATT --disable-colours
    # ===================================================================== #
    when /^-?-?disable(-|_)?colou?rs$/i
      disable_colours
    # ===================================================================== #
    # === levensthein --gap=
    # ===================================================================== #
    when /^-?-?gap=(.+)/
      set_gap_cost($1.to_s.dup)
    # ===================================================================== #
    # === levensthein --match=
    # ===================================================================== #
    when /^-?-?match=(.+)/
      set_match_cost($1.to_s.dup)
    # ===================================================================== #
    # === levensthein --mismatch=
    # ===================================================================== #
    when /^-?-?mismatch=(.+)/
      set_mismatch_cost($1.to_s.dup)
    end
  end
end

#mismatch_cost? ⇒ Boolean Also known as: score_for_mismatch?

#

mismatch_cost?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 491

def mismatch_cost?
  @internal_hash[:mismatch_cost]
end

#n_gaps? ⇒ Boolean

#

n_gaps?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 286

def n_gaps?
  @internal_hash[:n_gaps]
end

#n_matches? ⇒ Boolean

#

n_matches?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 272

def n_matches?
  @internal_hash[:n_matches]
end

#n_mismatches? ⇒ Boolean

#

n_mismatches?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 279

def n_mismatches?
  @internal_hash[:n_mismatches]
end

#parse_string1_and_string2(string1, string2) ⇒ Object

#

parse_string1_and_string2

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 472

def parse_string1_and_string2(
    string1, string2
  )
  if string1.is_a? Array
    menu(
      select_two_hyphens_from(string1)
    )
    remove_hyphens_from(string1)
  end
  if string1.is_a?(Array) and string2.nil? and (string1.size > 1)
    string2 = string1.pop
  end
  set_string1(string1)
  set_string2(string2)
end

#report_the_amount_of_mismatches_and_gaps ⇒ Object

#

report_the_amount_of_mismatches_and_gaps

This method will report how many mismatches and gaps can be found in the main sequence at hand.

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 644

def report_the_amount_of_mismatches_and_gaps
  the_string1 = string1?
  the_string2 = string2?
  # ======================================================================= #
  # First, report the amount of gaps:
  # ======================================================================= #
  if the_string2.include? '-'
    n_gaps = the_string2.count('-').to_s
  elsif the_string1.include? '-'
    n_gaps = the_string1.count('-').to_s
  end
  e
  erev 'The '+mediumseagreen('edit distance')+
       rev+
       ' (that is, only the '+
        slateblue('changes')+rev+') has exactly:'
  e
  plural_or_singular_of_gaps = 'gap'.dup
  plural_or_singular_of_gaps << 's' if n_gaps.to_i > 1
  erev ' '+n_gaps.to_s.rjust(2)+' '+
       plural_or_singular_of_gaps.ljust(11)+
       '(with a gap_cost of:      '+
       gap_cost?.to_s+')' # Report the gaps here, and their cost
  erev '  '+n_mismatches?.to_s+' mismatches '\
       '(with a mismatch_cost of: '+
       mismatch_cost?.to_s+')' # Report the mismatches here, and their cost
  e
end

#report_the_edit_distance ⇒ Object

#

report_the_edit_distance

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 462

def report_the_edit_distance
  erev 'The '+springgreen('Levensthein-distance')+
       rev+' (edit distance) between these '
  erev 'two strings is `'+sfancy(edit_distance?.to_s)+rev+
       '`. (Size of first string is: '+string1.size.to_s+')'
end

#report_the_total_cost ⇒ Object

#

report_the_total_cost

This method will calculate the total score.

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 521

def report_the_total_cost
  total_cost = 0
  total_cost += calculate_the_total_cost
  formatted_match_cost = match_cost?.to_s.dup
  unless formatted_match_cost.include? '-'
    formatted_match_cost.prepend('+')
  end
  erev 'The total cost (== score) is: '+sfancy(total_cost.to_s)+rev+' '\
       '(match cost was: '+formatted_match_cost+')'
  e
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 97

def reset
  super()
  # ======================================================================= #
  # === @namespace
  # ======================================================================= #
  @namespace = NAMESPACE
  # ======================================================================= #
  # === @be_verbose
  # ======================================================================= #
  @be_verbose = true
  # ======================================================================= #
  # === @internal_hash
  # ======================================================================= #
  @internal_hash = {}
  # ======================================================================= #
  # === :string1
  # ======================================================================= #
  @internal_hash[:string1] = nil
  # ======================================================================= #
  # === :string2
  # ======================================================================= #
  @internal_hash[:string2] = nil
  # ======================================================================= #
  # === :edit_distance
  # ======================================================================= #
  @internal_hash[:edit_distance] = 0
  # ======================================================================= #
  # === :initial_padding_to_use
  # ======================================================================= #
  @internal_hash[:initial_padding_to_use] = '  '
  # ======================================================================= #
  # Setup the default cost for a match, a mismatch and a gap.
  # ======================================================================= #
  set_match_cost
  set_mismatch_cost
  set_gap_cost
  reset_the_scores
end

#reset_the_scores ⇒ Object Also known as: reset_the_score

#

reset_the_scores

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 139

def reset_the_scores
  @internal_hash[:n_mismatches] = 0
  @internal_hash[:n_matches]    = 0
  @internal_hash[:n_gaps]       = 0
end

#run ⇒ Object

#

run

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 676

def run
  determine_the_edit_distance
  calculate_the_amount_of_mismatches_and_gaps
  do_report if be_verbose?
end

#set_gap_cost(i = DEFAULT_GAP_COST, optional_be_verbose = false) ⇒ Object Also known as: set_gap_score

#

set_gap_cost

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 200

def set_gap_cost(
    i                   = DEFAULT_GAP_COST,
    optional_be_verbose = false
  )
  i = i.to_i
  if optional_be_verbose == :be_verbose
    erev "Setting the gap cost to #{sfancy(i.to_s)}#{rev}"
  end
  @internal_hash[:gap_cost] = i
end

#set_match_cost(i = DEFAULT_MATCH_COST, optional_be_verbose = false) ⇒ Object Also known as: set_match_score

#

set_match_cost

This method sets the cost for a match.

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 183

def set_match_cost(
    i                   = DEFAULT_MATCH_COST,
    optional_be_verbose = false
  )
  if i.to_s.include? '+'
    i = i.to_s.delete('+')
  end
  i = i.to_i
  if optional_be_verbose == :be_verbose
    erev 'Setting the match cost to '+sfancy(i.to_s)+rev
  end
  @internal_hash[:match_cost] = i
end

#set_mismatch_cost(i = DEFAULT_MISMATCH_COST, optional_be_verbose = false) ⇒ Object Also known as: set_mismatch_score

#

set_mismatch_cost

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 233

def set_mismatch_cost(
    i                   = DEFAULT_MISMATCH_COST,
    optional_be_verbose = false
  )
  i = i.to_i
  if optional_be_verbose == :be_verbose
    erev 'Setting the mismatch cost to '+sfancy(i.to_s)+rev
  end
  @internal_hash[:mismatch_cost] = i
end

#set_string1(i = nil) ⇒ Object Also known as: string1=, set_sequence1

#

set_string1

This method can be used to assign the value to string1.

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 596

def set_string1(i = nil)
  if i.is_a? Array
    i = i.first
  end
  case i
  when :default_value,
       :default
    i = DEFAULT_STRING1
  end
  i = i.to_s.dup.chomp unless i.is_a? Symbol
  @internal_hash[:string1] = i
end

#set_string2(i = nil) ⇒ Object Also known as: string2=, set_sequence2

#

set_string2

This method can be used to assign the value to string2.

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 216

def set_string2(i = nil)
  if i.is_a? Array
    i = i.first
  end
  case i
  when :default_value,
       :default
    i = DEFAULT_STRING2
  end
  i = i.to_s.dup.chomp unless i.is_a? Symbol
  @internal_hash[:string2] = i
end

#show_first_string ⇒ Object

#

show_first_string

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 555

def show_first_string
  e orange(initial_padding_to_use?+string1?)
end

#show_help ⇒ Object

#

show_help (help tag)

Invoke this method via:

levensthein --show-help
#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 160

def show_help
  e
  erev 'You can use the following commandline-flag to read the scores '\
       'from an'
  erev 'existing file:'
  e
  e steelblue('  levensthein --use-this-file=/Depot/j/foo.md')
  e
  erev 'In order to use different costs, set interactively by the user, use:'
  e
  e steelblue('  levensthein --costs')
  e
  erev 'If you wish to start the gtk-GUI component, do:'
  e
  e steelblue('  levensthein --start-gui')
  e
end

#show_numbered_header ⇒ Object

#

show_numbered_header

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 536

def show_numbered_header
  length = string1.size
  result = ''.dup
  result << initial_padding_to_use?
  1.upto(length) {|number|
    if number > 9
      # =================================================================== #
      # In this case chop it down to below 10.
      # =================================================================== #
      number = number.to_s[-1,1].to_i
    end
    result << number.to_s
  }
  e lightgreen(result)
end

#show_second_string ⇒ Object

#

show_second_string

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 562

def show_second_string
  e orange(initial_padding_to_use?+string2?)
end

#string1? ⇒ Boolean Also known as: string1, sequence1?

#

string1

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 247

def string1?
  @internal_hash[:string1]
end

#string2? ⇒ Boolean Also known as: string2, sequence2?

#

string2

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 255

def string2?
  @internal_hash[:string2]
end

#try_to_read_sequences_from_this_file(i, be_verbose = true) ⇒ Object Also known as: read_sequences_from_this_file

#

try_to_read_sequences_from_this_file

This method can be used to read in one or two sequences from an existing file.

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 326

def try_to_read_sequences_from_this_file(
    i, be_verbose = true
  )
  if File.exist? i
    if be_verbose
      e "Trying to read in the sequence from the file `#{sfile(i)}`."
    end
    dataset = readlines(i)
    set_string1(dataset[0])
    set_string2(dataset[1]) if dataset.size > 1
  else
    no_file_exists_at(i)
  end
end

#try_to_use_this_file_as_input(i) ⇒ Object Also known as: use_this_file_for_score=

#

try_to_use_this_file_as_input

This method can be used to read from an existing file and assign match, mismatch and gap scores. This can be useful if you wish to NOT use the default hardcoded values in this class.

#

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# File 'lib/bioroebe/string_matching/levensthein.rb', line 348

def try_to_use_this_file_as_input(i)
  if File.exist? i
    dataset = file_readlines(i)
    dataset.each {|line|
      case line
      # ==================================================================== #
      # === gap
      # ==================================================================== #
      when /^gap:\s*(-?\d{1,4})/
        set_gap_cost($1, :be_verbose)
      # ==================================================================== #
      # === match
      # ==================================================================== #
      when /^match:\s*(-?\d{1,4})/
        set_match_cost($1, :be_verbose)
      # ==================================================================== #
      # === mismatch
      # ==================================================================== #
      when /^mismatch:\s*(-?\d{1,4})/
        set_mismatch_cost($1, :be_verbose)
      end
    }
  else
    no_file_exists_at(i)
  end
end