Class: Bioroebe::CheckForMismatches

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

Overview

Bioroebe::CheckForMismatches

Constant Summary collapse

COLOUR_TO_BE_USED_FOR_A_MISMATCH =
#

COLOUR_TO_BE_USED_FOR_A_MISMATCH

This constant can be used to colourize a mismatch. Make sure that this is a Symbol, ideally.

#
:tomato

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(input = ARGV, run_already = true) ⇒ CheckForMismatches

#

initialize

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 33

def initialize(
    input       = ARGV,
    run_already = true
  )
  reset
  set_commandline_input(input)
  run if run_already
end

Instance Method Details

#array_mismatches? ⇒ Boolean

#

array_mismatches?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 114

def array_mismatches?
  @array_mismatches
end

#chop_down_to_sequence_length(i) ⇒ Object

#

chop_down_to_sequence_length

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 149

def chop_down_to_sequence_length(i)
  if i.size > @first_sequence.size
    i = i[0, @first_sequence.size]
  end
  return i
end

#corresponding_nucleotide(i) ⇒ Object

#

corresponding_nucleotide

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 121

def corresponding_nucleotide(i)
  return_dna_match(i)
end

#get_user_input ⇒ Object

#

get_user_input

This method is to fetch user input.

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 90

def get_user_input
  opnerev 'Input your first sequence now:'
  first_sequence = $stdin.gets.chomp
  opnerev 'Input your second sequence now:'
  second_sequence = $stdin.gets.chomp
  set_data(first_sequence, second_sequence)
end

#handle_given_commandline_input(i = @commandline_input) ⇒ Object

#

handle_given_commandline_input

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 139

def handle_given_commandline_input(i = @commandline_input)
  unless i.empty?
    set_data(i)
    @obtain_user_input = false
  end
end

#report_results ⇒ Object Also known as: report

#

report_results (report tag)

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 166

def report_results
  mismatches = array_mismatches?
  if mismatches.empty?
    e
    erev 'We found no mismatch.'
    e
  else
    e
    erev swarn('Mismatches')+rev+' were found at the following locations:'
    e
    first_sequence  = @first_sequence
    second_sequence = @second_sequence
    colourized_first_sequence  = first_sequence.dup
    colourized_second_sequence = second_sequence.dup
    mismatches.each {|index, character|
      e rev+'  Position: '+simp(index.to_s)+rev+
        ', Nucleotide being: '+sfancy(character.to_s)
    }
    e
    array_mismatches?.reverse.each {|index, character|
      colourized_first_sequence[index-1,1]  = send(COLOUR_TO_BE_USED_FOR_A_MISMATCH, character)+
                                              rev
      corresponding_character = colourized_second_sequence[index-1,1]
      colourized_second_sequence[index-1,1] = send(COLOUR_TO_BE_USED_FOR_A_MISMATCH, corresponding_character)+
                                              rev
    }
    e "#{rev}The two strands were:"
    e
    e rev+
      "     "+
      turquoise(
        chop_down_to_sequence_length(
          return_one_to_ten+return_one_to_ten
        )
      )
    e rev+"  5'-"+colourized_first_sequence
    show_three_prime_colourized_sequence(colourized_second_sequence)
    e
  end
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 45

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @first_sequence
  # ======================================================================= #
  @first_sequence    = nil
  # ======================================================================= #
  # === @second_sequence
  # ======================================================================= #
  @second_sequence   = nil
  # ======================================================================= #
  # === @obtain_user_input
  # ======================================================================= #
  @obtain_user_input = true
  # ======================================================================= #
  # === @array_mismatches
  # ======================================================================= #
  @array_mismatches  = [] # This contains all mismatches.
end

#return_one_to_ten ⇒ Object

#

return_one_to_ten

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 159

def return_one_to_ten
  '1234567890'
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 217

def run
  get_user_input if @obtain_user_input
  opnerev 'We will now compare these two sequences'
  opnerev 'for any potential mismatch(es).'
  scan_for_mismatches
  report_results
end

#scan_for_mismatches ⇒ Object

#

scan_for_mismatches

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 101

def scan_for_mismatches
  @first_sequence.scan(/./).each_with_index {|character, index|
    result = corresponding_nucleotide(@second_sequence[index])
    if character == result # then all is fine
    else # else this is not fine so we spit out the problem.
      array_mismatches? << [index+1, character]
    end
  }
end

#set_commandline_input(i) ⇒ Object

#

set_commandline_input

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 128

def set_commandline_input(i)
  if i.is_a? Array
    i = i.join(' ').strip
  end
  @commandline_input = i.to_s.dup
  handle_given_commandline_input
end

#set_data(a = 'AAAAATTTTTCAAATTAA', b = 'TTTTTAAAAAATTTAAAA') ⇒ Object

#

set_data

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 69

def set_data( # Use this method to set the strand.
    a = 'AAAAATTTTTCAAATTAA',
    b = 'TTTTTAAAAAATTTAAAA'
  )
  if a.include? '|'
    # ===================================================================== #
    # In this case, split on it, and re-assign.
    # ===================================================================== #
    splitted = a.split('|').map(&:strip)
    a = splitted.first
    b = splitted.last
  end
  @first_sequence  = a.upcase # .allow_only_valid_dna
  @second_sequence = b.upcase # .allow_only_valid_dna
end

#show_three_prime_colourized_sequence(i) ⇒ Object

#

show_three_prime_colourized_sequence

#


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# File 'lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb', line 210

def show_three_prime_colourized_sequence(i)
  e rev+"  3'-"+i
end