bioroebe 0.10.80 → 0.12.12

data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb

@@ -2,65 +2,152 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
+# === Bioroebe::ConvertThisCodonToThatAminoacid
+#
+# This class can be used to convert a particular codon, such as 'ATG',
+# into the corresponding aminoacid, in this case being 'M' for
+# Methionin. A String will be returned by this method.
+#
+# The characters in that String will correspond to the one-letter
+# format of aminoacids, such as the example shown above 'M' for
+# Methionin.
+#
+# The method has to handle invalid input arguments as well, to some
+# extent.
+#
+# The method supports both DNA and mRNA as "input".
+#
+# In order for the method to do its job properly, the method will
+# make use of the codon table stored in:
+#
+#   Bioroebe.aa_to_rna_codon_table
+#
+# Also note that this method can easily be used to translate
+# other frames - simply provide the proper input to it.
+#
+# Note that this method will return the result - it will NOT 
+# output the result.
+#
+# Usage examples:
+#
+#   Bioroebe::ConvertThisCodonToThatAminoacid.new
+#   puts Bioroebe.codon_to_aminoacid('ATG')    # => "M"
+#   puts Bioroebe.codon_to_aminoacid('GUG')    # => "V"
+#   puts Bioroebe.decode_this_codon('CCG')     # => "P"
+#   puts Bioroebe.codon_to_aminoacid('GUGGUG') # => "VV"
+#   puts Bioroebe.codon_to_aminoacid('ATGA')   # => "M"
+#   puts Bioroebe.convert_dna_to_protein_sequence('ATGA') # => "M"
+#   puts Bioroebe.convert_this_codon_to_that_aminoacid('ATGA') # => "M"
+#
+# Commandline usage example:
+#
+#   dcodon TTT TTC # => ["TTY"]
+#
+# =========================================================================== #
 # require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
 # =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'
+
 module Bioroebe
 
+class ConvertThisCodonToThatAminoacid < ::Bioroebe::CommandlineApplication # === Bioroebe::ConvertThisCodonToThatAminoacid
+
   require 'bioroebe/codons/codon_table.rb'
 
   # ========================================================================= #
-  # === Bioroebe.convert_this_codon_to_that_aminoacid
-  #
-  # This method can be used to convert a particular codon, such as 'ATG',
-  # into the corresponding aminoacid, in this case being 'M' for
-  # Methionin. A String will be returned by this method.
-  #
-  # The characters in that String will correspond to the one-letter
-  # format of aminoacids, such as the example shown above 'M' for
-  # Methionin.
-  #
-  # The method has to handle invalid input arguments as well, to some
-  # extent.
-  #
-  # The method supports both DNA and mRNA as "input".
-  #
-  # In order for the method to do its job properly, the method will
-  # make use of the codon table stored in:
-  #
-  #   Bioroebe.aa_to_rna_codon_table
-  #
-  # Also note that this method can easily be used to translate
-  # other frames - simply provide the proper input to it.
-  #
-  # Note that this method will return the result - it will NOT 
-  # output the result.
-  #
-  # Usage examples:
-  #
-  #   puts Bioroebe.codon_to_aminoacid('ATG') # => "M"
-  #   puts Bioroebe.codon_to_aminoacid('GUG') # => "V"
-  #   puts Bioroebe.decode_this_codon('CCG')  # => "P"
-  #   puts Bioroebe.codon_to_aminoacid('GUGGUG') # => "VV"
-  #   puts Bioroebe.codon_to_aminoacid('ATGA') # => "M"
-  #   puts Bioroebe.convert_dna_to_protein_sequence('ATGA') # => "M"
-  #   puts Bioroebe.convert_this_codon_to_that_aminoacid('ATGA') # => "M"
-  #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = nil, # This should be an Array.
+      run_already = true,
+      &block
+    )
+    reset
+    set_commandline_arguments(i)
+    if block_given?
+      yielded = yield
+      case yielded
+      # ======================================================================= #
+      # === :be_quiet
+      # ======================================================================= #
+      when :be_quiet
+        be_quiet
+      end
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === @shall_we_replace_stop_codons
+    # ======================================================================= #
+    @shall_we_replace_stop_codons = :default
+    # ======================================================================= #
+    # === @with_trailer
+    # ======================================================================= #
+    @with_trailer = false
+  end
+
   # ========================================================================= #
-  def self.convert_this_codon_to_that_aminoacid(
-      i                            = ARGV,
-      shall_we_replace_stop_codons = :default,
-      use_this_codon_table         = codon_table_dataset?.dup
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      i = commandline_arguments_starting_with_a_hyphen?
     )
-    case shall_we_replace_stop_codons
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i # case tag
+      # ===================================================================== #
+      # === codon_to_aa --with-trailer
+      # ===================================================================== #
+      when /^-?-?with(-|_)?trailer$/i
+        @with_trailer = true
+      # ===================================================================== #
+      # === codon_to_aa --help
+      # ===================================================================== #
+      when /^-?-?help$/i
+        show_help
+        exit
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === show_help                                                  (help tag)
+  # ========================================================================= #
+  def show_help
+    e
+    e "  --with-trailer # display any result via 5'- and -3' padding"
+    e
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    i = commandline_arguments?
+    menu(
+      commandline_arguments_starting_with_a_hyphen(i)
+    )
+    case @shall_we_replace_stop_codons
+    # ======================================================================= #
+    # === :default
+    # ======================================================================= #
     when :default
-      shall_we_replace_stop_codons = true
+      @shall_we_replace_stop_codons = true
     end
     if i.is_a? Array
-      i = i.join
+      i = reject_hyphens(i).join
     end
     i = i.to_s.dup
     i.upcase!
     i.tr!('U','T') # We need DNA here, so U becomes T.
+    use_this_codon_table = codon_table_dataset?.dup
     # ======================================================================= #
     # Obtain the dataset from the correct codon_table next.
     # ======================================================================= #
@@ -80,23 +167,70 @@ module Bioroebe
     }
     result = scanned
     result = result.join if result.is_a? Array
-    return result
-  end; self.instance_eval { alias decode_this_codon               convert_this_codon_to_that_aminoacid } # === Bioroebe.decode_this_codon
-       self.instance_eval { alias convert_dna_to_protein_sequence convert_this_codon_to_that_aminoacid } # === Bioroebe.convert_dna_to_protein_sequence
-       self.instance_eval { alias translate_dna_into_aminoacid    convert_this_codon_to_that_aminoacid } # === Bioroebe.translate_dna_into_aminoacid
-       self.instance_eval { alias dna_to_aa                       convert_this_codon_to_that_aminoacid } # === Bioroebe.dna_to_aa
-       self.instance_eval { alias codon_to_aminoacid              convert_this_codon_to_that_aminoacid } # === Bioroebe.codon_to_aminoacid
+    if @with_trailer
+      result = result.dup
+      result.prepend("5'-")
+      result << "-3'"
+    end
+    @result = result
+    report
+  end
+
+  # ========================================================================= #
+  # === report
+  # ========================================================================= #
+  def report
+    e @result if be_verbose?
+  end
+
+  # ========================================================================= #
+  # === result?
+  # ========================================================================= #
+  def result?
+    @result
+  end; alias sequence? result? # === sequence?
+
+  # ========================================================================= #
+  # === Bioroebe::ConvertThisCodonToThatAminoacid[]
+  #
+  # Usage example:
+  #
+  #   Bioroebe::ConvertThisCodonToThatAminoacid[]
+  #
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i).result?
+  end
+
+end
+
+# =========================================================================== #
+# === Bioroebe.convert_this_codon_to_that_aminoacid
+# =========================================================================== #
+def self.convert_this_codon_to_that_aminoacid(i = ARGV)
+  Bioroebe::ConvertThisCodonToThatAminoacid.new(i) { :be_quiet }
+end; self.instance_eval { alias decode_this_codon               convert_this_codon_to_that_aminoacid } # === Bioroebe.decode_this_codon
+     self.instance_eval { alias convert_dna_to_protein_sequence convert_this_codon_to_that_aminoacid } # === Bioroebe.convert_dna_to_protein_sequence
+     self.instance_eval { alias translate_dna_into_aminoacid    convert_this_codon_to_that_aminoacid } # === Bioroebe.translate_dna_into_aminoacid
+     self.instance_eval { alias dna_to_aa                       convert_this_codon_to_that_aminoacid } # === Bioroebe.dna_to_aa
+     self.instance_eval { alias codon_to_aminoacid              convert_this_codon_to_that_aminoacid } # === Bioroebe.codon_to_aminoacid
 
 end
 
 if __FILE__ == $PROGRAM_NAME
   alias e puts
-  # pp Bioroebe.convert_this_codon_to_that_aminoacid(ARGV)
-  # pp Bioroebe.convert_this_codon_to_that_aminoacid(ARGV)
-  e 'GUGGUG → '+Bioroebe.codon_to_aminoacid('GUGGUG') # => "VV"
-  e 'ATG → '+Bioroebe.codon_to_aminoacid('ATG') # => "M"
-  e 'GUG → '+Bioroebe.codon_to_aminoacid('GUG') # => "V"
-  e 'CCG → '+Bioroebe.decode_this_codon('CCG')  # => "P"
-  e 'ATGA → '+Bioroebe.codon_to_aminoacid('ATGA') # => "M"
-  e 'ATGA → '+Bioroebe.convert_dna_to_protein_sequence('ATGA') # => "M"
-end # $RUBY_SRC/bioroebe/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb
+  if ARGV.empty?
+    # ======================================================================= #
+    # pp Bioroebe.convert_this_codon_to_that_aminoacid(ARGV)
+    # pp Bioroebe.convert_this_codon_to_that_aminoacid(ARGV)
+    # ======================================================================= #
+    e 'GUGGUG → '+Bioroebe.codon_to_aminoacid('GUGGUG') # => "VV"
+    e 'ATG    → '+Bioroebe.codon_to_aminoacid('ATG')    # => "M"
+    e 'GUG    → '+Bioroebe.codon_to_aminoacid('GUG')    # => "V"
+    e 'CCG    → '+Bioroebe.decode_this_codon('CCG')     # => "P"
+    e 'ATGA   → '+Bioroebe.codon_to_aminoacid('ATGA')   # => "M"
+    e 'ATGA   → '+Bioroebe.convert_dna_to_protein_sequence('ATGA') # => "M"
+  else
+    _ = Bioroebe::ConvertThisCodonToThatAminoacid.new(ARGV)
+  end
+end # ConvertThisCodonToThatAminoacid GGT GGC

data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb

@@ -27,11 +27,6 @@ class PossibleCodonsForThisAminoacid < ::Bioroebe::CommandlineApplication # ===
 
   require 'bioroebe/codons/codon_table.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === SHOW_ADDITIONAL_HINTS
   #
@@ -93,10 +88,7 @@ class PossibleCodonsForThisAminoacid < ::Bioroebe::CommandlineApplication # ===
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @try_to_identify_purines_and_pyrimidines
     # ======================================================================= #

data/lib/bioroebe/codons/show_codon_tables.rb

@@ -37,6 +37,7 @@ class ShowCodonTables < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowC
     else
       first = show_what
     end
+    first = first.to_s.delete('-')
     case first.to_sym
     # ======================================================================= #
     # === :human
@@ -56,7 +57,9 @@ class ShowCodonTables < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowC
          :headers,
          '--headers'
       ::Bioroebe::CodonTables.definitions?.each_pair {|number, long_name|
-        e number.to_s.rjust(3)+') '+long_name.ljust(70)
+        e turquoise(number.to_s.rjust(3))
+          +') '+
+          long_name.ljust(70)
       }
     end
   end
@@ -127,4 +130,5 @@ end
 if __FILE__ == $PROGRAM_NAME
   Bioroebe::ShowCodonTables.new(ARGV)
 end # showcodontables
-    # showcodontables human
+    # showcodontables human
+    # showcodontables everything

data/lib/bioroebe/codons/show_codon_usage.rb

@@ -24,6 +24,7 @@ module Bioroebe
 class ShowCodonUsage < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowCodonUsage
 
   require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+  require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
 
   # ========================================================================= #
   # === initialize
@@ -133,12 +134,13 @@ class ShowCodonUsage < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowCo
   # ========================================================================= #
   def report_the_top_five_codons(from_this_dataset)
     e
-    e 'The top five codons in use, sorted, are:'
+    erev 'The '+mediumpurple('top five codons')+
+         rev+' in use, sorted by frequency, are:'
     e
     top_five = from_this_dataset.sort_by {|key, values| values }.reverse[0..4]
     top_five.each {|name_of_codon, how_many_of_them|
       _ = name_of_codon.upcase
-      this_codon = codon_to_aminoacid(_)
+      this_codon = codon_to_aminoacid(_).sequence?
       colourized_this_codon = turquoise(this_codon)
       e rev+'  - '+
         teal(_)+
@@ -184,10 +186,19 @@ end
 
 # =========================================================================== #
 # === Bioroebe.codon_frequencies_of_this_sequence
+#
+# Usage example:
+#
+#   x = Bioroebe.codon_frequencies_of_this_sequence('ATGGGCGGGGTGATGGCAATGCCTTTAATGCCGCCAAAAAAAAAAAAAAAA')
+#
+# Will yield this Hash:
+#
+#   {"AAA"=>5, "ATG"=>4, "CCA"=>1, "CCG"=>1, "TTA"=>1, "CCT"=>1, "GCA"=>1, "GTG"=>1, "GGG"=>1, "GGC"=>1}
+#
 # =========================================================================== #
 def self.codon_frequencies_of_this_sequence(i = ARGV)
-  Bioroebe::ShowCodonUsage.new(i) { :be_quiet }
-end
+  Bioroebe::ShowCodonUsage.new(i) { :be_quiet }.result?
+end; self.instance_eval { alias hash_frequencies codon_frequencies_of_this_sequence } # === Bioroebe.hash_frequencies
 
 end
 

data/lib/bioroebe/colours/rev.rb

@@ -17,7 +17,10 @@ module Bioroebe
   # ========================================================================= #
   def self.rev
     if @use_colours
-      return Colours::GREEN # Default colour goes in here.
+      unless Object.const_defined?(:Colours)
+        require 'colours'
+      end
+      return ::Colours::GREEN # Default colour goes in here.
     end
     return ''
   end

data/lib/bioroebe/constants/aminoacids_and_proteins.rb

@@ -3,6 +3,7 @@
 # frozen_string_literal: true
 # =========================================================================== #
 # require 'bioroebe/constants/aminoacids_and_proteins.rb'
+# Bioroebe.filter_away_invalid_aminoacids
 # =========================================================================== #
 module Bioroebe
 

data/lib/bioroebe/constants/database_constants.rb

@@ -89,7 +89,7 @@ module Postgresql # === Bioroebe::Postgresql
   DROP_TABLE_FASTA = 'DROP TABLE fasta;'
 
   # ========================================================================= #
-  # === POSTGRE_DROP_FASTA_COMMAND
+  # === Bioroebe::Postgresql::POSTGRE_DROP_FASTA_COMMAND
   # ========================================================================= #
   POSTGRE_DROP_FASTA_COMMAND = DROP_FASTA_TABLE = DROP_TABLE_FASTA
 

data/lib/bioroebe/constants/files_and_directories.rb

@@ -165,15 +165,23 @@ module Bioroebe
   end
 
   # ========================================================================= #
-  # === FILE_FASTQ_QUALITY_SCHEMES
+  # === Bioroebe.fasta_dir?
+  # ========================================================================= #
+  def self.fasta_dir?
+    "#{Bioroebe.log_dir?}fasta/"
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.file_fastq_quality_schemes
   #
   # This constant will point to a location such as this one here:
   #
   #   /Programs/Ruby/2.6.4/lib/ruby/site_ruby/2.6.0/bioroebe/yaml/fastq_quality_schemes.yml
   #
   # ========================================================================= #
-  FILE_FASTQ_QUALITY_SCHEMES =
-    "#{project_yaml_directory?}fastq_quality_schemes.yml"
+  def self.file_fastq_quality_schemes
+    "#{project_yaml_directory?}fasta_and_fastq/fastq_quality_schemes.yml"
+  end
 
   # ========================================================================= #
   # === Bioroebe.file_talens
@@ -318,10 +326,17 @@ module Bioroebe
   # ========================================================================= #
   # === Bioroebe.file_restriction_enzymes
   # ========================================================================= #
-  def file_restriction_enzymes
+  def self.file_restriction_enzymes
     FILE_RESTRICTION_ENZYMES
   end
 
+  # ========================================================================= #
+  # === file_restriction_enzymes
+  # ========================================================================= #
+  def file_restriction_enzymes
+    ::Bioroebe.file_restriction_enzymes
+  end
+
   # ========================================================================= #
   # === Bioroebe.blosum_directory?
   # ========================================================================= #
@@ -553,6 +568,18 @@ module Bioroebe
     "#{project_yaml_directory?}aminoacids/molecular_weight.yml"
   end
 
+  # ========================================================================= #
+  # === Bioroebe.file_amino_acids_long_name_to_one_letter
+  #
+  # This method will return a String such as:
+  #
+  #   "/home/Programs/Ruby/3.1.2/lib/ruby/site_ruby/3.1.0/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml"
+  #
+  # ========================================================================= #
+  def self.file_amino_acids_long_name_to_one_letter
+    "#{project_yaml_directory?}aminoacids/amino_acids_long_name_to_one_letter.yml"
+  end
+
 end
 
 if __FILE__ == $PROGRAM_NAME

data/lib/bioroebe/constants/misc.rb

@@ -43,6 +43,26 @@ module Bioroebe
   # ========================================================================= #
   TOKEN = '|'
 
+  # ========================================================================= #
+  # === VALID_WAYS_TO_EXIT
+  #
+  # All ways to exit will be recorded here.
+  #
+  # If you need to use more ways, simply append to this Array.
+  #
+  # This constant may have to be moved into the bio-shell part eventually.
+  # ========================================================================= #
+  VALID_WAYS_TO_EXIT = %w(
+    quit q exit qq :q qt
+    bye
+    rda
+    r2
+    tq
+    sq
+    exit_program
+    exitprogram
+  )
+
   # ========================================================================= #
   # === NAMES_ENTRIES
   #

data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb

@@ -40,6 +40,7 @@ module Bioroebe
 class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::DnaToAminoacidSequence
 
   require 'bioroebe/codons/codon_table.rb'
+  require 'bioroebe/misc/ruler.rb'
 
   # ========================================================================= #
   # === DEFAULT_RUN_MODE
@@ -63,8 +64,9 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     if block_given?
       yielded = yield
       case yielded
+      # === :be_verbose
       when :be_verbose
-        @be_verbose = true
+        set_be_verbose
       when :be_quiet
         be_quiet
       end
@@ -155,6 +157,10 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     # ======================================================================= #
     @internal_hash[:report_result] = true
     # ======================================================================= #
+    # === :show_ruler
+    # ======================================================================= #
+    @internal_hash[:show_ruler] = false
+    # ======================================================================= #
     # === :show_as_three_letter_aminoacid_sequence
     #
     # If this is true then this class will show "Phe" rather than "F" for
@@ -188,7 +194,7 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
   # === be_quiet
   # ========================================================================= #
   def be_quiet
-    @be_verbose = false
+    set_be_quiet
     @internal_hash[:report_result] = false
   end
 
@@ -307,7 +313,10 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
       )
     end
     set_result(result)
-    if report_result? and @be_verbose
+    if report_result? and be_verbose?
+      if show_ruler? # Show a pretty ruler here.
+        e "  #{Bioroebe.return_ruler(i)}"
+      end
       e "  #{@result}"
       e N
     end
@@ -339,23 +348,6 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     ]
   end
 
-  # ========================================================================= #
-  # === show_help                                                  (help tag)
-  # ========================================================================= #
-  def show_help
-    e 'Available options:'
-    e
-    e '  --gui                           # start the GUI'
-    e '  --stop-at-the-first-stop-codon  # stop at the first stop codon encountered'
-    e '  --frame1                        # show the first frame translation only'
-    e '  --frame2                        # show the second frame translation only'
-    e '  --frame3                        # show the third frame translation only'
-    e '  --use-this-codon-table=bacteria # specify a specific codon table '\
-      '(in this case bacteria)'
-    e '  --three-letter                  # show the three letter amino acid code'
-    e
-  end
-
   # ========================================================================= #
   # === menu                                                       (menu tag)
   #
@@ -372,6 +364,16 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     else
       case i
       # ===================================================================== #
+      # === Show a helpful ruler
+      #
+      # Usage example:
+      #
+      #   dnatoaminoacidsequence AUGUUU --ruler
+      #
+      # ===================================================================== #
+      when /^-?-?ruler$/i
+        do_show_ruler
+      # ===================================================================== #
       # === Show the aminoacids as three-letter code
       #
       # Usage example:
@@ -496,14 +498,33 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
       #
       # The result is stored in the variable called @result.
       # ===================================================================== #
-      translated_codon = translate_dna_into_aminoacid(this_codon)
-      @result << translated_codon.to_s
+      translated_codon = translate_dna_into_aminoacid(this_codon).to_s
+      @result << translated_codon
       if @stop_at_the_first_stop_codon and (translated_codon == '*')
         break
       end
     }
   end
 
+  # ========================================================================= #
+  # === show_help                                                  (help tag)
+  # ========================================================================= #
+  def show_help
+    e 'Available options:'
+    e
+    e '  --gui                           # start the GUI'
+    e '  --stop-at-the-first-stop-codon  # stop at the first stop codon encountered'
+    e '  --frame1                        # show the first frame translation only'
+    e '  --frame2                        # show the second frame translation only'
+    e '  --frame3                        # show the third frame translation only'
+    e '  --use-this-codon-table=bacteria # specify a specific codon table '\
+      '(in this case bacteria)'
+    e '  --three-letter                  # show the three letter amino acid code'
+    e '  --ruler                         # show a helpful ruler on top '\
+      'of the sequence'
+    e
+  end
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
@@ -512,6 +533,20 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     do_the_conversion_step
     report
   end
+ 
+  # ========================================================================= #
+  # === do_show_ruler
+  # ========================================================================= #
+  def do_show_ruler
+    @internal_hash[:show_ruler] = true
+  end
+
+  # ========================================================================= #
+  # === show_ruler?
+  # ========================================================================= #
+  def show_ruler?
+    @internal_hash[:show_ruler]
+  end
 
   # ========================================================================= #
   # === Bioroebe::DnaToAminoacidSequence[]
@@ -556,8 +591,7 @@ if __FILE__ == $PROGRAM_NAME
   if _.empty?
     _ = 'ATGCGTAAAGGAGAAGAACTTTTCACTTGGAGTTGTCCCAATTCTTGTTGGGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACATACGGAAAACTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCGGTTATGGTGTTCAATGCTTTGCGAGATACCCAGATCATATGAAACAGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAAAGAACTATATTTTTCAAAGATGACGGGAACTACAAGACACGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATAGAATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAATTGGAATACAACTATAACTCACACAATGTATACATCATGGCAGACAAACAAAAGAATGGAATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGAAGCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGAGAGACCACATGGTCCTTCTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGGATGAACTATACAAATAG'
   end
-  Bioroebe.erev 'The input-sequence was: '+
-                 _.join
+  Bioroebe.erev('The input-sequence was: '+_)
   Bioroebe::DnaToAminoacidSequence.new(_)
   e
   e 'Next, all three frames will be translated:'