Class: Bioroebe::CalculateBlosumScore

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/calculate/calculate_blosum_score.rb

Overview

Bioroebe::CalculateBlosumScore

Constant Summary collapse

GAP_OPEN_COST =
#

GAP_OPEN_COST

Two constants to define initially the cost for gap-open and gap-extension costs.

#
-12
GAP_EXTENSION_COST =
#

GAP_EXTENSION_COST

#
-2

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(parse_this_input = nil) ⇒ CalculateBlosumScore

#

initialize

The input to initialite should be a String.

#


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# File 'lib/bioroebe/calculate/calculate_blosum_score.rb', line 41

def initialize(
    parse_this_input = nil
  )
  reset
  # ======================================================================= #
  # === Default to BLOSUM50
  #
  # Determine which blosum-dataset to use next:
  # ======================================================================= #
  blosum50_dataset = Bioroebe::BlosumParser.new(FILE_BLOSUM50)
  @hash = blosum50_dataset.hash
  if parse_this_input # If we provided an Argument, we will assume this to be a String, and parse it.
    parse_input(parse_this_input)
  end
end

Instance Method Details

#parse_input(i, be_verbose = :be_quiet) ⇒ Object Also known as: test

#

parse_input

We parse the given input here. This should be in the form of an Aminoacid-chain, but we will also handle input that is

#


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# File 'lib/bioroebe/calculate/calculate_blosum_score.rb', line 78

def parse_input(
    i, be_verbose = :be_quiet
  )
  if be_verbose == :be_verbose
    erev "Working on the input String: \n"+steelblue(i)+rev
  end
  i = i.strip
  array_that_holds_our_two_aminoacids = i.split(N).map(&:strip).reject(&:empty?)
  first_array  = array_that_holds_our_two_aminoacids.first.chars
  second_array = array_that_holds_our_two_aminoacids[1].chars
  this_is_the_input = first_array.zip(second_array).map {|entry| entry.join }
  score = 0 # We assume the initial score to be 0.
  @found_a_gap = false
  this_is_the_input.each {|entry|
    if @hash.has_key? entry
      @found_a_gap = false
      score += @hash[entry].to_i
    else # This here handles gaps.
      # We must distinguish between a gap-open cost and a gap extension
      # cost.
      if @found_a_gap # If this is already true, then it must be a gap-extension.
        score += @gap_extension_cost
      else # Else it must be a gap-open cost.
        score += @gap_open_cost
      end
      @found_a_gap = true
    end
  }
  set_score(score) # Store the result for the score as well.
  e score
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/calculate/calculate_blosum_score.rb', line 60

def reset
  super()
  # ======================================================================= #
  # === @gap_open_cost
  # ======================================================================= #
  @gap_open_cost      = GAP_OPEN_COST
  # ======================================================================= #
  # === @gap_extension_cost
  # ======================================================================= #
  @gap_extension_cost = GAP_EXTENSION_COST
end

#score? ⇒ Boolean Also known as: result?

#

score?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/calculate/calculate_blosum_score.rb', line 120

def score?
  @score
end

#set_score(i) ⇒ Object

#

set_score

#


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# File 'lib/bioroebe/calculate/calculate_blosum_score.rb', line 113

def set_score(i)
  @score = i # Keep track of the score here.
end