Class: Bioroebe::CompareTheseTwoSequencesViaBlosum

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

Overview

Bioroebe::CompareTheseTwoSequencesViaBlosum

Constant Summary collapse

USE_THIS_FILE =
#

USE_THIS_FILE

#
'/home/x/Temp/bioroebe/blosum50.yml'

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

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, #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 = nil, run_already = true) ⇒ CompareTheseTwoSequencesViaBlosum

#

initialize

#


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# File 'lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb', line 32

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

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::CompareTheseTwoSequencesViaBlosum[]

#


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# File 'lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb', line 111

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

Instance Method Details

#do_work_through_these_two_sequences(a, b) ⇒ Object

#

do_work_through_these_two_sequences

#


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# File 'lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb', line 66

def do_work_through_these_two_sequences(a, b)
  dataset = @internal_hash[:dataset]
  b_chars = b.chars
  total_score = 0
  gap_is_open = false
  be_verbose = be_verbose?
  a.chars.each_with_index {|char, index|
    char1 = char
    char2 = b_chars[index]
    if char1 == '-' or char2 == '-'
      if gap_is_open
        total_score += (-2)
        if be_verbose
          erev 'Gap extension cost for the two elements '+char1+char2+
            ' total score is now: '+tomato(total_score.to_s)+rev+')'
        end
      else
        total_score += (-12)
        if be_verbose
          erev 'Gap open cost for the two elements '+char1+char2+
            ' total score is now: '+tomato(total_score.to_s)+rev+')'
        end
      end
      gap_is_open = true
    else
      gap_is_open = false # Always close it then.
      value = dataset[char1 + char2]
      total_score += value
      if be_verbose
        erev 'Normal BLOSUM50 cost for the two elements '+
          char1+char2+' '+
          tomato(
            '(add '+value.to_s+
            ' total score is now: '+total_score.to_s+')'
          )+rev
      end
      
    end
  }
  erev 'The final score of these two sequences is '+royalblue(total_score)+rev+'.'
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb', line 44

def reset
  super()
  # ======================================================================= #
  # === :dataset
  # ======================================================================= #
  @internal_hash[:dataset] = YAML.load_file(USE_THIS_FILE)
  set_be_quiet # Or set_be_verbose
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb', line 56

def run
  _ = commandline_arguments?
  sequence1 = _[0]
  sequence2 = _[1]
  do_work_through_these_two_sequences(sequence1, sequence2)
end