Class: Bioroebe::ShowThisCodonTable

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

Constant Summary collapse

LPAD =
#

LPAD

#
'  '
MPAD =
#

MPAD

#
'      '
CYAN =
#

CYAN

#
Colours::CYAN
CYAN_U = 
CYAN+'U'
CYAN_A = 
CYAN+'A'
CYAN_G = 
CYAN+'G'
CYAN_C = 
CYAN+'C'
ARRAY_ALL_CODONS =
#

CodonTable::ARRAY_ALL_CODONS (array tag)

This Array will be used to batch-define the necessary methods.

#
%w(

  TTT? TTC? TTA? TTG?
  TCT? TCC? TCA? TCG?
  TAT? TAC? TAA? TAG?
  TGT? TGC? TGA? TGG?

  CTT? CCT? CAT? CGT?
  CTC? CCC? CAC? CGC?
  CTA? CCA? CAA? CGA?
  CTG? CCG? CAG? CGG?

  ATT? ACT? AAT? AGT?
  ATC? ACC? AAC? AGC?
  ATA? ACA? AAA? AGA?
  ATG? ACG? AAG? AGG?

  GTT? GCT? GAT? GGT?
  GTC? GCC? GAC? GGC?
  GTA? GCA? GAA? GGA?
  GTG? GCG? GAG? GGG?

)
STOP =
#

STOP

The stop codon.

#
Colours::RED+'STOP'+Colours::GREEN
DEFAULT_CODON_TABLE_TO_USE =
#

DEFAULT_CODON_TABLE_TO_USE

#
:human

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

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, #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(commandline_arguments = ARGV, run_already = true) ⇒ ShowThisCodonTable

#

initialize

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 99

def initialize(
    commandline_arguments = ARGV,
    run_already           = true
  )
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  run if run_already
end

Instance Method Details

#colourized_line(i) ⇒ Object

#

colourized_line

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 344

def colourized_line(i)
  result = i.dup.gsub(/\*/, stop?).
                 gsub(/START/, '*').
                 squeeze('*').
                 gsub(/\*/,tomato('*')+rev)
  e result
  i
end

#consider_using_a_specific_codon_table(i = first_argument?) ) ⇒ Object

#

consider_using_a_specific_codon_table

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 205

def consider_using_a_specific_codon_table(i = first_argument?)
  set_use_this_codon_table(i)
end

#cyan ⇒ Object

#

cyan

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 198

def cyan
  CYAN # This will work, as CYAN has been defined in this file.
end

#cyana ⇒ Object Also known as: cyan_a, cyan_A

#

cyana

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 182

def cyana
  cyan+'A'+rev
end

#cyanc ⇒ Object Also known as: cyan_c, cyan_C

#

cyanc

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 485

def cyanc
  cyan+'C'+rev
end

#cyang ⇒ Object Also known as: cyan_g, cyan_G

#

cyang

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 190

def cyang
  cyan+'G'+rev
end

#cyanu ⇒ Object Also known as: cyan_U, cyan_u, cyan_T

#

cyanu

This will either show a U or a T.

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 465

def cyanu
  case @show_rna_or_dna
  # ======================================================================= #
  # === :rna
  # ======================================================================= #
  when :rna
    "#{cyan}U#{rev}"
  # ======================================================================= #
  # === :dna
  # ======================================================================= #
  when :dna
    "#{cyan}T#{rev}"
  end
end

#dataset? ⇒ Boolean

#

dataset?

#

Returns:

  • (Boolean) 


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

def dataset?
  ::Bioroebe.codon_table_dataset?
end

#determine_all_codon_methods(dataset = dataset? ) ⇒ Object

#

determine_all_codon_methods

Dynamically define the proper methods.

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 302

def determine_all_codon_methods(
    dataset = dataset?
  )
  start_codons = dataset['START']
  if start_codons.include? '|'
    start_codons = start_codons.split('|').map(&:strip)
  end
  if @autogenerate_codon_related_methods
    dataset = dataset?
    ARRAY_ALL_CODONS.each {|entry|
      entry = entry.to_sym
      # =================================================================== #
      # We will only define these methods once.
      # =================================================================== #
      unless self.respond_to? entry
        # ================================================================= #
        # We define methods on this class, such as .GGG? and similar.
        # ================================================================= #
        self.class.instance_eval {
          define_method(entry) {
            name_of_the_codon = __method__.to_s.chop
            if dataset.has_key? name_of_the_codon
              result = dataset.fetch(name_of_the_codon)
              result = stop? if result == '*'
              if start_codons.include? name_of_the_codon
                result << 'START'
              end
            else
              result = 'UNKNOWN (from '+name_of_the_codon+')'
            end
            return result
          }
        }
      end
    }
    @autogenerate_codon_related_methods = false
  end
end

#determine_dataset ⇒ Object

#

determine_dataset

This method will determine the correct codon-dataset. It has to make sure that the codon table actually exists, though.

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 429

def determine_dataset
  # ======================================================================= #
  # We must set the correct title to use, if no argument was provided.
  # ======================================================================= #
  if title?.nil? and first_argument?.nil?
    set_title("Standard (Eukaryote) Codon Table")
    set_codon_table(1)
  end
  this_codon_table = use_which_codon_table?
  if this_codon_table.is_a?(String) and (this_codon_table =~ /^\d+$/)
    title = ::Bioroebe::CodonTables.definitions?[this_codon_table.to_i]
    set_title(title)  
  end
end

#display_title ⇒ Object

#

display_title

This method will show the title of the codon table in question.

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 415

def display_title
  title = title?
  if title
    erev title+' (codon table number: '+
         steelblue(codon_table?.to_s)+rev+'):'
  end
end

#green ⇒ Object Also known as: rev

#

green

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 168

def green
  Colours::GREEN
end

#is_this_codon_table_available?(i) ⇒ Boolean

#

is_this_codon_table_available?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 212

def is_this_codon_table_available?(i)
  target = directory_to_the_codon_tables?+"#{i}.yml"
  return File.exist?(target)
end

#left_pad ⇒ Object

#

left_pad

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 515

def left_pad
  print '  ' 
end

#lpad(i) ⇒ Object

#

lpad

#


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

def lpad(i)
  if i.include? 'STOP'
    i+'   '
  elsif i.include? 'START'
    i+'     '
  else
    i+'      '
  end
end

#lpad? ⇒ Boolean

#

lpad?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 233

def lpad?
  LPAD
end

#lpad_on(*i) ⇒ Object

#

lpad_on

This method combines several calls such as this:

lpad(TTC?)+lpad(TCC?)+lpad(TAC?)+lpad(TGC?)

It was too long, so it was changed to.

lpad_on(TTT?, TCT?, TAT?, TGT?)
#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 293

def lpad_on(*i)
  i.map {|entry| lpad(entry) }.join
end

#menu(i = @commandline_arguments) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 356

def menu(
    i = @commandline_arguments
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === codontable --rna
    #
    # This variant will display the table as "RNA".
    #
    # Invocation examples:
    #
    #   ctable --rna
    #   ctable 1 --rna
    #
    # ===================================================================== #
    when /^-?-?rna$/i
      @show_rna_or_dna = :rna
      @commandline_arguments.reject! {|entry| entry.to_s =~ /^-?-?rna$/i }
    else
      if i.to_s =~ /^(\d{1,2})-(\d{1,2})$/
        # ================================================================= #
        #   ctable 1-3
        # ================================================================= #
        $1.to_i.upto($2.to_i) {|n|
          consider_using_a_specific_codon_table(n)
          determine_dataset
          determine_all_codon_methods
          display_codon_table
        }
        exit
      elsif i.to_s =~ /^\d{1,2}$/
        # ================================================================= #
        # Need to convert into a real number.
        #
        # Usage Examples:
        #
        #   ctable 1
        #   ctable 3
        #   ctable 1-2
        #
        # ================================================================= #
        require 'bioroebe/codons/codon_tables.rb'
        @commandline_arguments[0] = i.to_i
        set_title(
          Bioroebe::CodonTables.title_for_entry_number?(i.to_i)
        )
      end
    end
  end
end

#notify_the_user_that_no_such_codon_table_could_be_found ⇒ Object

#

notify_the_user_that_no_such_codon_table_could_be_found

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 447

def notify_the_user_that_no_such_codon_table_could_be_found
  erev 'No codon table matching this input ('+
       steelblue(first_argument?.to_s)+
       rev+') could be found.'
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 113

def reset
  super()
  # ======================================================================= #
  # === :title
  # ======================================================================= #
  @internal_hash[:title] = nil
  # ======================================================================= #
  # === @is_available
  #
  # This instance variable keeps track as to whether the given coden
  # table is available or whether it is not, based on a number. For
  # some reasons, probably historic reasons, some numbers are missing.
  #
  # By default this variable is true, but it will be set to false if
  # the input can not be correlated to an existing codon table.
  # ======================================================================= #
  @is_available = false
  # ======================================================================= #
  # === @show_rna_or_dna
  #
  # This variable can be either :dna or :rna.
  #
  # The default is :dna. If you wish to set this to :rna on the commandline
  # then you can use "codontable --rna".
  # ======================================================================= #
  @show_rna_or_dna = :dna
  # ======================================================================= #
  # === @autogenerate_codon_related_methods
  # ======================================================================= #
  @autogenerate_codon_related_methods = true
end

#return_dataset_from_codon_table(this_codon_table = use_which_codon_table? ) ⇒ Object

#

return_dataset_from_codon_table

This method will return the dataset from the codon table.

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 257

def return_dataset_from_codon_table(
    this_codon_table = use_which_codon_table?
  )
  if this_codon_table.is_a?(String) and (this_codon_table =~ /^\d+$/)
    this_codon_table = this_codon_table.to_i
    set_codon_table(this_codon_table)
  end
  ::Bioroebe.codon_table_dataset?
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 556

def run
  menu
  consider_using_a_specific_codon_table
  determine_dataset
  determine_all_codon_methods
  if @is_available
    display_codon_table
  else
    notify_the_user_that_no_such_codon_table_could_be_found
  end
end

#set_codon_table(i) ⇒ Object

#

set_codon_table

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 270

def set_codon_table(i)
  ::Bioroebe.set_codon_table(i)
end

#set_title(i = nil) ⇒ Object

#

set_title

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 148

def set_title(
    i = nil
  )
  if i and i.is_a?(String)
    i = i.dup if i.frozen?
    i << ' Codon Table' unless i.end_with?(' Codon Table')
  end
  # ======================================================================= #
  # === :title
  #
  # @title will keep track of the title of the specific codon table.
  # That is, every codon table has a specific name such as "Standard
  # Eukaryotic Table".
  # ======================================================================= #
  @internal_hash[:title] = i
end

#set_use_this_codon_table(i = DEFAULT_CODON_TABLE_TO_USE) ⇒ Object

#

set_use_this_codon_table

This will initially hold the codon table internally.

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 495

def set_use_this_codon_table(
    i = DEFAULT_CODON_TABLE_TO_USE
  )
  require 'bioroebe/codons/codon_table.rb'
  i = i.first if i.is_a? Array
  case i
  when 'human'
    i = 1
  when nil
    i = DEFAULT_CODON_TABLE_TO_USE
  end
  if is_this_codon_table_available?(i)
    @is_available = true
    ::Bioroebe.set_use_this_codon_table(i)
  end
end

#stop? ⇒ Boolean

#

stop?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 175

def stop?
  STOP
end

#title? ⇒ Boolean

#

title?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 277

def title?
  @internal_hash[:title]
end

#top_row_header ⇒ Object

#

top_row_header

#


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 456

def top_row_header
  e cyan+N+LPAD+'      '+cyanu+MPAD+cyanc+MPAD+cyana+MPAD+cyang
end

#use_this_codon_table? ⇒ Boolean Also known as: use_which_codon_table?, codon_table?

#

use_this_codon_table?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/show_this_codon_table.rb', line 240

def use_this_codon_table?
  ::Bioroebe.codon_table?
end