Class: Bioroebe::DotAlignment

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

Overview

Bioroebe::DotAlignment

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 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(i = nil, run_already = true) ⇒ DotAlignment

#

initialize

#

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# File 'lib/bioroebe/utility_scripts/dot_alignment.rb', line 27

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

Class Method Details

.[](i = '') ⇒ Object

#

Bioroebe::DotAlignment[]

#

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

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

Instance Method Details

#determine_the_two_sequences_that_are_to_be_compared(sequence1 = commandline_arguments?[0], sequence2 = commandline_arguments?[1]) ⇒ Object

#

determine_the_two_sequences_that_are_to_be_compared

#

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# File 'lib/bioroebe/utility_scripts/dot_alignment.rb', line 100

def determine_the_two_sequences_that_are_to_be_compared(
    sequence1 = commandline_arguments?[0],
    sequence2 = commandline_arguments?[1]
  )
  @sequence1 = sequence1.to_s.strip
  @sequence2 = sequence2.to_s.strip
  # ======================================================================= #
  # We must check if the first argument is actually a file.
  # ======================================================================= #
  if File.file? @sequence1
    # ===================================================================== #
    # In this case we read in the dataset of said file.
    # ===================================================================== #
    @dataset = File.readlines(@sequence1).map {|entry|
      entry.to_s.strip
    }.reject {|line| line.strip.empty? }
    # ===================================================================== #
    # Next, we do batch-comparisons.
    # ===================================================================== #
    @dataset.each_cons(2) {|a, b|
      reset_result
      do_compare_the_two_sequences(a, b)
      report(a, b)
      e # And a newline for "cleanness".
    }
    @may_we_continue = false
  end
end

#do_compare_the_two_sequences(sequence1 = @sequence1, sequence2 = @sequence2) ⇒ Object

#

do_compare_the_two_sequences

#

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# File 'lib/bioroebe/utility_scripts/dot_alignment.rb', line 132

def do_compare_the_two_sequences(
    sequence1 = @sequence1,
    sequence2 = @sequence2
  )
  sequence1.chars.each_with_index {|char, index|
    if char == sequence2[index]
      @result << '*'
    else
      @result << ' '
    end
  }
end

#report(sequence1 = seq1?, , sequence2 = seq2? ) ⇒ Object

#

report (report tag)

Note that this class will report the length of the two sequences as well.

#

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# File 'lib/bioroebe/utility_scripts/dot_alignment.rb', line 85

def report(
    sequence1 = seq1?,
    sequence2 = seq2?
  )
  erev @left_padding_to_use+
       steelblue(sequence1)+royalblue(" # #{sequence1.size.to_s}")
  erev @left_padding_to_use+
       steelblue(sequence2)+royalblue(" # #{sequence2.size.to_s}")
  erev @left_padding_to_use+
       sfancy(@result)
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/utility_scripts/dot_alignment.rb', line 39

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @may_we_continue
  # ======================================================================= #
  @may_we_continue = true
  reset_result
  # ======================================================================= #
  # === @left_padding_to_use
  # ======================================================================= #
  @left_padding_to_use = '  '
end

#reset_result ⇒ Object

#

reset_result

#

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

def reset_result
  # ======================================================================= #
  # === @result
  #
  # This will be the result-string that is shown to the user.
  # ======================================================================= #
  @result = ''.dup
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/utility_scripts/dot_alignment.rb', line 148

def run
  determine_the_two_sequences_that_are_to_be_compared
  if @may_we_continue
    do_compare_the_two_sequences
    report
  end
end

#seq1? ⇒ Boolean Also known as: seq1

#

seq1?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/utility_scripts/dot_alignment.rb', line 68

def seq1?
  @sequence1
end

#seq2? ⇒ Boolean Also known as: seq2

#

seq2?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/utility_scripts/dot_alignment.rb', line 75

def seq2?
  @sequence2
end