Class: Bioroebe::PossibleCodonsForThisAminoacid

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb

Overview

Bioroebe::PossibleCodonsForThisAminoacid

Constant Summary collapse

SHOW_ADDITIONAL_HINTS =
#

SHOW_ADDITIONAL_HINTS

If this constant is set to true, then we will additionally give some hints for the user about grouping purines and pyrimidines.

#
true
CODON_TABLE =
#

CODON_TABLE

#
::Bioroebe.codon_table?
ARRAY_PURINES =
#

ARRAY_PURINES

#
%w( A G )
ARRAY_PYRIMIDINES =
#

ARRAY_PYRIMIDINES

#
%w( T C )
TRY_TO_IDENTIFY_PURINES_AND_PYRIMIDINES =
#

TRY_TO_IDENTIFY_PURINES_AND_PYRIMIDINES

If this constant is set to true then we will attempt to group purines and pyrimidines.

#
true

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, #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) ⇒ PossibleCodonsForThisAminoacid

#

initialize

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 64

def initialize(
    i           = nil,
    run_already = true
  )
  reset
  set_input(i)
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :do_not_simplify_purines_and_pyrimidines
    # ===================================================================== #
    when :do_not_simplify_purines_and_pyrimidines
      do_not_simplify_purines_and_pyrimidines
    end
  end
  run if run_already
end

Class Method Details

.[](i = '', replace_purines_and_pyrimidines = true) ⇒ Object

#

Bioroebe::PossibleCodonsForThisAminoacid[]

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 306

def self.[](i = '', replace_purines_and_pyrimidines = true)
  _ = new(i, :do_not_run_yet)
  case replace_purines_and_pyrimidines
  when :use_only_the_four_standard_nucleotide_letters
    replace_purines_and_pyrimidine = false
  end
  unless replace_purines_and_pyrimidine
    _.set_try_to_identify_purines_and_pyrimidines false 
  end
  _.run
  return _.keys
end

.translate(i) ⇒ Object

#

Bioroebe::PossibleCodonsForThisAminoacid.translate

This method will conveniently return the Array that has the corresponding codons.

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 299

def self.translate(i)
  new(i).possible_codons?
end

Instance Method Details

#array_like_result? ⇒ Boolean Also known as: pretty_result

#

array_like_result?

This method will report in an array-like manner.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 241

def array_like_result?
  "[#{result?}]"
end

#do_not_simplify_purines_and_pyrimidines ⇒ Object

#

do_not_simplify_purines_and_pyrimidines

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 166

def do_not_simplify_purines_and_pyrimidines
  set_try_to_identify_purines_and_pyrimidines(false)
end

#input? ⇒ Boolean

#

input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 138

def input?
  @input
end

#is_purin?(i) ⇒ Boolean Also known as: is_purine?

#

is_purin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 152

def is_purin?(i)
  ARRAY_PURINES.include? i
end

#is_pyrimidin?(i) ⇒ Boolean Also known as: is_pyrimidine?

#

is_pyrimidin?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 145

def is_pyrimidin?(i)
  ARRAY_PYRIMIDINES.include? i
end

#one_letter_to_full_name(i) ⇒ Object

#

one_letter_to_full_name

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 213

def one_letter_to_full_name(i)
  ::Bioroebe.convert_one_letter_to_full(i)
end

#original_input? ⇒ Boolean

#

original_input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 102

def original_input?
  @original_input
end

#possible_codons? ⇒ Boolean Also known as: keys?, keys, results?, array_as_result

#

possible_codons?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 229

def possible_codons?
  @possible_codons
end

#report_result ⇒ Object Also known as: report

#

report_result

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 173

def report_result
  codon_singular_or_plural = 'codon'.dup
  codon_singular_or_plural << 's' if keys?.size > 1
  # ======================================================================= #
  # Build up the String that we will output.
  # ======================================================================= #
  one_letter_to_full_name = steelblue("#{one_letter_to_full_name(original_input?).capitalize}")+
                            rev
  result = "#{rev}The aminoacid #{simp(original_input?)}#{rev} "\
           "(#{one_letter_to_full_name}) "\
           "may be encoded by ".dup
  if keys?.size > 1
    result << 'these'
  else
    result << 'this'
  end
  result << rev+
            ' '+
            royalblue(keys?.size.to_s)+
            rev+
            ' nucleotide '+codon_singular_or_plural+
            ":\n\n"
  result << "  #{sfancy(array_like_result?)}#{rev}\n\n"

  # ======================================================================= #
  # Display the result next:
  # ======================================================================= #
  e result
  if SHOW_ADDITIONAL_HINTS
    if result?.include? 'Y'
      e '(Note that pyrimidines are denoted by the letter "Y").'
    elsif result?.include? 'R' 
      e '(Note that purines are denoted by the letter "R").'
    end
  end
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 89

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @try_to_identify_purines_and_pyrimidines
  # ======================================================================= #
  @try_to_identify_purines_and_pyrimidines =
    TRY_TO_IDENTIFY_PURINES_AND_PYRIMIDINES
end

#result? ⇒ Boolean

#

result?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 220

def result?
  _ = keys?.join(',')
  _.chop! if _.end_with? ','
  _
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 283

def run
  # ======================================================================= #
  # Grab a handle to the codon table next.
  # ======================================================================= #
  possible_codons = Bioroebe.codon_table_dataset?.select {|key, value|
    key if value == input?
  }
  set_possible_codons(possible_codons.keys)
end

#set_input(i = '') ⇒ Object

#

set_input

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 109

def set_input(i = '')
  i = i.first if i.is_a? Array
  i = i.to_s.dup
  @original_input = i.dup
  # ======================================================================= #
  # The keys are downcased, so we downcase the input as well.
  # ======================================================================= #
  i.downcase!
  # ======================================================================= #
  # The following constant is a Hash, and it will have key->value pairs
  # such as "cysteine"=>"C".
  # ======================================================================= #
  if i.size > 1 # Assume that the user input the long name here.
    if AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.has_key? i
      i = AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER[i]
    elsif AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.has_key? i.chop # Try with the last char chopped off.
      i = AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER[i.chop]
    end
  end
  # ======================================================================= #
  # We want the input upcased past this point.
  # ======================================================================= #
  i.upcase!
  @input = i
end

#set_possible_codons(i = nil) ⇒ Object

#

set_possible_codons

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 248

def set_possible_codons(i = nil)
  # ======================================================================= #
  # Replace with shorter variants if the following variable is true.
  # ======================================================================= #
  if @try_to_identify_purines_and_pyrimidines
    i.map! {|entry| entry.to_s.dup }
    # ===================================================================== #
    # First check on purines.
    # ===================================================================== #
    last_characters = i.map {|entry| entry.chars.last }
    if last_characters.all? {|entry| is_purin?(entry) }
      # =================================================================== #
      # Ok, the last ones are all Purines here.
      # =================================================================== #
      i.map! {|entry|
        entry[-1,1] = 'R' # Adenin or Guanin.
        entry
      }
    elsif last_characters.all? {|entry| is_pyrimidin?(entry) }
      # =================================================================== #
      # Ok, the last ones are all Pyrimidines here. Y is the shortcut.
      # =================================================================== #
      i.map! {|entry|
        entry[-1,1] = 'Y' # # Cytosin or Thymin. 
        entry
      }
    end
  end
  i.uniq!
  @possible_codons = i
end

#set_try_to_identify_purines_and_pyrimidines(i) ⇒ Object

#

set_try_to_identify_purines_and_pyrimidines

#


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# File 'lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb', line 159

def set_try_to_identify_purines_and_pyrimidines(i)
  @try_to_identify_purines_and_pyrimidines = i
end