RubyGems - bioroebe - Versions diffs - 0.10.80 → 0.11.32 - Mend

bioroebe 0.10.80 → 0.11.32

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data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb ADDED Viewed

@@ -0,0 +1,164 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Colourize
+#
+# This file can be used to colourize a string representing DNA (in fasta
+# format), for use (or display) on a website. HTML colour code and CSS
+# rules will be used.
+#
+# The colour to use can be passed via the second method to four of the
+# module-level methods in this file.
+# =========================================================================== #
+module Bioroebe
+module Colourize # === Bioroebe::Colourize
+  require 'bioroebe/colours/colours.rb'
+  require 'bioroebe/toplevel_methods/e.rb'
+  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
+  # ========================================================================= #
+  # === Bioroebe::Colourize.generate_HTML_page_via_this_input
+  #
+  # This method will generate a .html page, using the default colourization
+  # rules defined in this file here.
+  # ========================================================================= #
+  def self.generate_HTML_page_via_this_input(i)
+    if i.is_a? Array
+      i = i.join(' ').strip
+    end
+    what = "<!DOCTYPE html>\n<html lang=\"en\"><head>"\
+           "<title>Colourized FASTA Sequence</title><style>\n".dup
+    what << "#{return_default_CSS_rules_to_use}\n\n"
+    what << "</style>\n</head>\n<body>\n"
+    result = colourize_this_FASTA_sequence(i)
+    what << "#{result}</body></html>\n"
+    # ======================================================================= #
+    # The name of the generated file is determined by the input
+    # argument given.
+    # ======================================================================= #
+    into = File.basename(i).delete_suffix(File.extname(i))+
+           '.html'
+    if File.exist? into
+      e 'Can not store into an already existing file.'
+    else
+      e 'Storing into the file '+::Bioroebe.sfile(into)+' next.'
+      ::Bioroebe.write_what_into(what, into)
+    end
+  end
+  # ========================================================================= #
+  # === Bioroebe::Colourize.return_default_CSS_rules_to_use
+  # ========================================================================= #
+  def self.return_default_CSS_rules_to_use
+    return '.lightgreen {
+  color: lightgreen;
+}
+.lightblue {
+  color: lightblue;
+}
+.mediumslateblue {
+  color: lightblue;
+}
+.olivedrab {
+  color: olivedrab;
+}
+body {
+  background-color: black;
+  color: white;
+  font-family: monospace;
+  font-size: 2em;
+}'
+  end
+  # ========================================================================= #
+  # === Bioroebe::Colourize.colourize_this_FASTA_sequence
+  # ========================================================================= #
+  def self.colourize_this_FASTA_sequence(
+      i = ARGV
+    )
+    if i.is_a? Array
+      i = i.join(' ').strip
+    end
+    if i and File.file?(i)
+      # unless Bioroebe.const_defined?(:ParseFasta)
+      #   require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+      # end
+      # i = Bioroebe::ParseFasta.new(i) { :be_quiet }.sequence?
+      i = File.readlines(i).reject {|line|
+        line.start_with?('#','>')
+      }.join("\n")
+    end
+    result = colourize_TUG_start_codon(i)
+    result = colourize_TAG_stop_codon(result)
+    result = colourize_TAA_stop_codon(result)
+    result = colourize_TGA_stop_codon(result)
+    return result
+  end
+  # ========================================================================= #
+  # === Bioroebe::Colourize.colourize_TAG_stop_codon
+  # ========================================================================= #
+  def self.colourize_TAG_stop_codon(
+      i               = '',
+      use_this_colour = :lightblue
+    )
+    return i.gsub(
+      /(TA\n?G)/,
+      '<span class="'+use_this_colour.to_s+'">\1</span>'
+    )
+  end
+  # ========================================================================= #
+  # === Bioroebe::Colourize.colourize_TAA_stop_codon
+  # ========================================================================= #
+  def self.colourize_TAA_stop_codon(
+      i               = '',
+      use_this_colour = :lightgreen
+    )
+    return i.gsub(
+      /(TA\n?A)/,
+      '<span class="'+use_this_colour.to_s+'">\1</span>'
+    )
+  end
+  # ========================================================================= #
+  # === Bioroebe::Colourize.colourize_TGA_stop_codon
+  # ========================================================================= #
+  def self.colourize_TGA_stop_codon(
+      i               = '',
+      use_this_colour = :olivedrab
+    )
+    return i.gsub(
+      /(TG\n?A)/,
+      '<span class="'+use_this_colour.to_s+'">\1</span>'
+    )
+  end
+  # ========================================================================= #
+  # === Bioroebe::Colourize.colourize_TUG_start_codon
+  # ========================================================================= #
+  def self.colourize_TUG_start_codon(
+      i               = '',
+      use_this_colour = :mediumslateblue
+    )
+    return i.gsub(
+      /(TU\n?G)/,
+    '<span class="'+use_this_colour.to_s+'">\1</span>'
+    )
+  end
+end; end
+if __FILE__ == $PROGRAM_NAME
+  alias e puts
+  # e Bioroebe::Colourize.colourize_this_FASTA_sequence(ARGV)
+  Bioroebe::Colourize.generate_HTML_page_via_this_input(ARGV)
+end # colourizerelatedmethods alu_elements.fasta

data/lib/bioroebe/toplevel_methods/databases.rb CHANGED Viewed

@@ -15,7 +15,7 @@ module Bioroebe
   # can pass the password for the postgreSQL database.
   # ========================================================================= #
   def self.set_pgpassword(
-      new_password = POSTGRE_PASSWORD
+      new_password = Bioroebe::Postgresql::POSTGRE_PASSWORD
     )
     ENV['PGPASSWORD'] = new_password
   end; self.instance_eval { alias set_password set_pgpassword } # === Bioroebe.set_password

data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb CHANGED Viewed

@@ -49,68 +49,6 @@ module Bioroebe
     end
   end
-  # ========================================================================= #
-  # === Bioroebe.colourize_this_fasta_dna_sequence
-  #
-  # This toplevel method can be used to colourize a FASTA (DNA)
-  # sequence, e. g. "ATGCGCGTATTA" and so forth.
-  #
-  # Note that this is intended for the commandline, that is to be
-  # displayed on e. g. a KDE Konsole terminal.
-  #
-  # Usage example:
-  #
-  #   puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA')
-  #
-  # ========================================================================= #
-  def self.colourize_this_fasta_dna_sequence(
-      i = nil
-    )
-    if i.nil?
-      e 'Please provide a valid FASTA sequence as input to '\
-        'Bioroebe.colourize_this_fasta_dna_sequence()'
-      return
-    end
-    if i.is_a? Array
-      # ===================================================================== #
-      # Arrays will be joined together.
-      # ===================================================================== #
-      i = i.join(' ').strip
-    end
-    if i.is_a? String
-      # ===================================================================== #
-      # The colours are either defined in a file called
-      # 'colourize_fasta_sequences.yml' or they are simply hardcoded.
-      #
-      # The preferred (and thus default) way is to simply make use
-      # of that .yml file. That works on my home system, so it
-      # should work for other people as well.
-      # ===================================================================== #
-      if use_colours?
-        i = i.dup if i.frozen?
-        this_file = FILE_COLOURIZE_FASTA_SEQUENCES
-        if File.exist? this_file
-          dataset_for_the_colours = YAML.load_file(this_file)
-          dataset_for_the_colours.each_pair {|this_nucleotide, this_colour_to_be_used|
-            i.gsub!(
-              /#{this_nucleotide}/,
-              send(this_colour_to_be_used, this_nucleotide)+
-              rev
-            )
-          }
-        else
-          i.gsub!(/A/, "#{teal('A')}#{rev}")
-          i.gsub!(/C/, "#{slateblue('C')}#{rev}")
-          i.gsub!(/G/, "#{royalblue('G')}#{rev}")
-          i.gsub!(/T/, "#{steelblue('T')}#{rev}")
-          i.gsub!(/U/, "#{steelblue('U')}#{rev}") # Uracil is just the same as Thymine.
-        end
-      end
-    end
-    i
-  end; self.instance_eval { alias colourize_this_fasta_sequence colourize_this_fasta_dna_sequence } # === Bioroebe.colourize_this_fasta_sequence
-       self.instance_eval { alias colourized_parse_fasta        colourize_this_fasta_dna_sequence } # === Bioroebe.colourized_parse_fasta
   # ========================================================================= #
   # === Bioroebe.calculate_weight_of_the_aminoacids_in_this_fasta_file
   #
@@ -317,13 +255,119 @@ module Bioroebe
     end
   end
+  # ========================================================================= #
+  # === Bioroebe.colourize_this_fasta_dna_sequence
+  #
+  # This toplevel method can be used to colourize a FASTA (DNA)
+  # sequence, e. g. "ATGCGCGTATTA" and so forth.
+  #
+  # Note that this is intended for the commandline, that is to be
+  # displayed on e. g. a KDE Konsole terminal.
+  #
+  # Usage examples:
+  #
+  #   puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA')
+  #   puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA') { :with_ruler }
+  #   puts Bioroebe.colourize_this_fasta_dna_sequence('TGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA') { :with_ruler_steelblue_colour }
+  #
+  # ========================================================================= #
+  def self.colourize_this_fasta_dna_sequence(
+      i = nil,
+      &block
+    )
+    unless ::Bioroebe.respond_to?(:ruler_return_as_string_without_colours)
+      require 'bioroebe/misc/ruler.rb'
+    end
+    if i.nil?
+      e 'Please provide a valid FASTA sequence as input to '\
+        'Bioroebe.colourize_this_fasta_dna_sequence()'
+      return
+    end
+    if i.is_a? Array
+      # ===================================================================== #
+      # Arrays will be joined together.
+      # ===================================================================== #
+      i = i.join(' ').strip
+    end
+    # ======================================================================= #
+    # Check for existing files next:
+    # ======================================================================= #
+    if i and File.file?(i)
+      i = File.read(i)
+    end
+    original_input = i.dup
+    i = i.dup # Always dup it here.
+    if i.is_a? String
+      # ===================================================================== #
+      # The colours are either defined in a file called
+      # 'colourize_fasta_sequences.yml' or they are simply hardcoded.
+      #
+      # The preferred (and thus default) way is to simply make use
+      # of that .yml file. That works on my home system, so it
+      # should work for other people as well.
+      # ===================================================================== #
+      if use_colours?
+        this_file = FILE_COLOURIZE_FASTA_SEQUENCES
+        if File.exist? this_file
+          dataset_for_the_colours = YAML.load_file(this_file)
+          dataset_for_the_colours.each_pair {|this_nucleotide, this_colour_to_be_used|
+            i.gsub!(
+              /#{this_nucleotide}/,
+              Colours.send(this_colour_to_be_used, this_nucleotide)+
+              rev
+            )
+          }
+        else
+          i.gsub!(/A/, "#{teal('A')}#{rev}")
+          i.gsub!(/C/, "#{slateblue('C')}#{rev}")
+          i.gsub!(/G/, "#{royalblue('G')}#{rev}")
+          i.gsub!(/T/, "#{steelblue('T')}#{rev}")
+          i.gsub!(/U/, "#{steelblue('U')}#{rev}") # Uracil is just the same as Thymine.
+        end
+      end
+    end
+    # ======================================================================= #
+    # === Handle blocks next
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+      case yielded
+      # ===================================================================== #
+      # === with_ruler
+      # ===================================================================== #
+      when :with_ruler,
+           :add_ruler,
+           :ruler
+        i.prepend(
+          ::Bioroebe.ruler_return_as_string_without_colours(original_input)+
+          "\n"
+        )
+      else # Assume something like:
+           #   :with_ruler_steelblue_colour
+        if yielded.to_s.include? 'colo' # This assumes "colour" or "color".
+          use_this_colour = yielded.to_s.sub(/_colou?r/,'').
+                                         sub(/with_ruler_/,'')
+          this_string = send(use_this_colour,
+            ::Bioroebe.ruler_return_as_string_without_colours(original_input)+
+            "\n"
+          )
+          i.prepend(this_string)
+        end
+      end
+    end
+    return i
+  end; self.instance_eval { alias colourize_this_fasta_sequence colourize_this_fasta_dna_sequence } # === Bioroebe.colourize_this_fasta_sequence
+       self.instance_eval { alias colourized_parse_fasta        colourize_this_fasta_dna_sequence } # === Bioroebe.colourized_parse_fasta
   # ========================================================================= #
   # === Bioroebe.show_fasta_header
   #
   # This ad-hoc method can be used to quickly show the first line of an
   # assumed .fasta file.
   # ========================================================================= #
-  def self.show_fasta_header(of_this_file)
+  def self.show_fasta_header(
+      of_this_file
+    )
     if of_this_file.is_a? Array
       of_this_file = of_this_file.first
     end

data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb CHANGED Viewed

@@ -13,6 +13,13 @@ module Bioroebe
   require 'bioroebe/colours/sfile.rb'
   require 'bioroebe/colours/sdir.rb'
+  # ========================================================================= #
+  # === Bioroebe.move_file
+  # ========================================================================= #
+  def self.move_file(a, b)
+    FileUtils.mv(a, b)
+  end
   # ========================================================================= #
   # === Bioroebe.pwd                                                (pwd tag)
   #
@@ -134,6 +141,9 @@ module Bioroebe
       be_verbose = false
     )
     case be_verbose
+    # ======================================================================= #
+    # === :do_report_current_directory
+    # ======================================================================= #
     when :do_report_current_directory,
          :be_verbose
       be_verbose = true
@@ -160,12 +170,14 @@ module Bioroebe
     # Bioroebe.save_dir? is defined in bioroebe/toplevel_methods/store_here.rb.
     # ======================================================================= #
     when 'base',
-         'logdir'
+         'logdir',
+         :bioroebe_log_directory
       # ===================================================================== #
       # Enter the main log dir, unless a file exists with the same name.
       # ===================================================================== #
-      i = save_dir? unless File.exist? i
+      i = save_dir? unless File.exist?(i.to_s) # .to_s to avoid Symbols here.
     end
+    i = i.dup if i.is_a?(String) and i.frozen?
     i << '/' unless i.end_with? '/'
     if File.directory? i
       e sdir(i) if be_verbose # Also colourize the directory and output it.

data/lib/bioroebe/toplevel_methods/misc.rb CHANGED Viewed

@@ -14,21 +14,41 @@ module Bioroebe
   require 'bioroebe/toplevel_methods/e.rb'
   require 'bioroebe/toplevel_methods/esystem.rb'
   require 'bioroebe/toplevel_methods/extract.rb'
+  #require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
   # ========================================================================= #
-  # === Bioroebe.thousand_percentage
+  # === Bioroebe.create_jar_archive
+  #
+  # This method will create a .jar file.
+  #
+  # To invoke it from the commandline do:
+  #
+  #   bioroebe --jar
+  #
+  # To execute a .jar file do:
+  #
+  #   java -jar foobar.jar
   #
-  # This method is solely a helper-method for Bioroebe.frequency_per_thousand().
   # ========================================================================= #
-  def self.thousand_percentage(
-      this_codon_n_times =   1,
-      total_n_elements  = 1000
-    )
-    result = (
-      (this_codon_n_times * 1000.0) / total_n_elements.to_f
-    ).round(1)
-    padded_result = result.to_s.rjust(5, ' ')
-    return padded_result
+  def self.create_jar_archive
+    e 'Creating a .jar archive next:'
+    e
+    original_dir = return_pwd
+    cd '/home/x/programming/ruby/src/bioroebe/lib/bioroebe/java/bioroebe/src/main/java/'
+    esystem 'jar cf bioroebe.jar bioroebe/'
+    target_file = File.absolute_path('bioroebe.jar')
+    cd original_dir
+    if File.exist? target_file
+      e 'Moving the created .jar file into the current working '\
+        'directory next.'
+      move_file(target_file, original_dir)
+      e 'It should now be at:'
+      e
+      e sfile("  #{original_dir}#{File.basename(target_file)}")
+      e
+    end
+#   esystem 'jar cfe bioroebe.jar myClass myClass.class'
+    e
   end
   # ========================================================================= #
@@ -86,6 +106,7 @@ EOF
   # Usage example:
   #
   #   Bioroebe.codon_frequency_of_this_string
+  #   Bioroebe.codon_frequency_of_this_string 'ATTCGTACGATCGACTACTACT' # => {"UAC"=>2, "GAC"=>1, "AUC"=>1, "ACG"=>1, "CGU"=>1, "AUU"=>1}
   #
   # ========================================================================= #
   def self.codon_frequency_of_this_string(
@@ -107,6 +128,22 @@ EOF
     return sorted_hash
   end
+  # ========================================================================= #
+  # === Bioroebe.thousand_percentage
+  #
+  # This method is solely a helper-method for Bioroebe.frequency_per_thousand().
+  # ========================================================================= #
+  def self.thousand_percentage(
+      this_codon_n_times =   1,
+      total_n_elements  = 1000
+    )
+    result = (
+      (this_codon_n_times * 1000.0) / total_n_elements.to_f
+    ).round(1)
+    padded_result = result.to_s.rjust(5, ' ')
+    return padded_result
+  end
   # ========================================================================= #
   # === Bioroebe.align_this_string_via_multiple_sequence_alignment
   #
@@ -420,6 +457,76 @@ EOF
   end; self.instance_eval { alias on_windows?    windows_platform? } # === Bioroebe.on_windows?
        self.instance_eval { alias is_on_windows? windows_platform? } # === Bioroebe.is_on_windows?
+  # ========================================================================= #
+  # === Bioroebe.two_dimensional_plot
+  #
+  # This method makes use of gnuplot to draw a 2D plot.
+  #
+  # The first argument should contain your dataset, as a String.
+  # ========================================================================= #
+  def self.two_dimensional_plot(
+      dataset =  '6 12
+8 14
+10 18
+12 23
+14 28
+16 29
+18 26
+20 23
+22 20',
+      optional_hash = {
+        width:    800,
+        height:   640
+      }
+    )
+    # ======================================================================= #
+    # Provide some generic fall-back values for width and height next:
+    # ======================================================================= #
+    width  = 1000
+    height =  800
+    _ = optional_hash
+    if _.is_a? Hash
+      # ===================================================================== #
+      # === :width
+      # ===================================================================== #
+      if _.has_key? :width
+        width = _.delete(:width)
+      end
+      # ===================================================================== #
+      # === :height
+      # ===================================================================== #
+      if _.has_key? :height
+        height = _.delete(:height)
+      end
+    end
+    # ======================================================================= #
+    # Go to a safe base directory.
+    # ======================================================================= #
+    cd :bioroebe_log_directory
+    mkdir 'gnuplot' unless File.directory?('gnuplot')
+    cd 'gnuplot'
+    # ======================================================================= #
+    # First save the dataset into dataset.md:
+    # ======================================================================= #
+    into = File.absolute_path('dataset.md')
+    e 'Storing the dataset into '+sfile(into)+' next.'
+    write_what_into(dataset, into)
+    what = <<-EOF
+set terminal png size #{width},#{height} enhanced font "Helvetica, 18"
+set output 'fancy_graph.png'
+plot '#{into}' with linespoints ls 1 notitle
+EOF
+    into = File.absolute_path('gnuplot.file')
+    e 'Storing into '+into+'.'
+    write_what_into(what, into)
+    esystem 'gnuplot '+into
+    if File.exist? 'fancy_graph.png' and is_on_roebe?
+      Open.in_browser('fancy_graph.png')
+    end
+  end
 end
 if __FILE__ == $PROGRAM_NAME

data/lib/bioroebe/toplevel_methods/nucleotides.rb CHANGED Viewed

@@ -270,12 +270,19 @@ module Bioroebe
   #   Bioroebe.random_dna 15 # => "TTGGTAAGCTCTTTA"
   #   Bioroebe.random_dna 25 # => "TTAGCACAAGCATGGACGGACCAGA"
   #   Bioroebe.random_dna(50, { A: 10, T: 10, C: 10, G: 70}) # => "GGGGTGGGGAGGGTATGCGGAGGAAGGGCGGGAAGGGCGGGGGCTGGGCG"
+  #   Bioroebe.random_dna(20, 'ATGGGGGGGG') # => "TGAGGGGGGGGGTGGGAGGG"
+  #   Bioroebe.random_dna(20, 'ATGGGGGGGG') # => "GGTAGGGGGGGGTAGGGGGG"
   #
   # ========================================================================= #
   def self.generate_random_dna_sequence(
-      i = ARGV,
-      optional_hash_with_the_frequencies = {}
+      i                                  = ARGV,
+      optional_hash_with_the_frequencies = {} # ← This may be a String too, mind you.
     )
+    # ======================================================================= #
+    # First define our result-String. This one will be returned by this
+    # method.
+    # ======================================================================= #
+    result = ''.dup
     _ = Bioroebe::DNA_NUCLEOTIDES # Get a handle to the four DNA nucleotides.
     if i.is_a? Array
       i = i.join.strip
@@ -284,9 +291,19 @@ module Bioroebe
     when :default
       i = 250
     end
-    i = i.to_i
-    result = ''.dup
-    if optional_hash_with_the_frequencies.empty?
+    i = i.to_i # This is "n times".
+    # ======================================================================= #
+    # First handle the case where the user passed a String:
+    # ======================================================================= #
+    if optional_hash_with_the_frequencies.is_a? String
+      pool = optional_hash_with_the_frequencies.dup.chars.shuffle
+      i.times {
+        if pool.size == 0
+          pool = optional_hash_with_the_frequencies.dup.chars.shuffle
+        end
+        result << pool.pop
+      }
+    elsif optional_hash_with_the_frequencies.empty?
       # ===================================================================== #
       # This is the default clause.
       # ===================================================================== #

data/lib/bioroebe/toplevel_methods/open_in_browser.rb CHANGED Viewed

@@ -18,6 +18,8 @@ module Bioroebe
   # This constant specifies the default browser to use for the
   # bioroebe-project.
   # ========================================================================= #
+  # /home/x/programming/ruby/src/bioroebe/lib/bioroebe/yaml/configuration/browser.yml
+  # ========================================================================= #
   if File.exist? "#{project_yaml_directory?}browser.yml"
     USE_THIS_BROWSER = YAML.load_file(FILE_BROWSER)
   elsif ENV['BROWSER']

data/lib/bioroebe/toplevel_methods/palindromes.rb CHANGED Viewed

@@ -115,8 +115,7 @@ module Bioroebe
 end
 if __FILE__ == $PROGRAM_NAME
-pp Bioroebe.every_reverse_palindrome_in_this_string(ARGV)
-exit
+  pp Bioroebe.every_reverse_palindrome_in_this_string(ARGV)
   if ARGV.empty?
     p 'GAATTC: '+Bioroebe.is_palindrome?('GAATTC').to_s   # => true
     p 'GAATTCCC: '+Bioroebe.is_palindrome?('GAATTCCC').to_s # => false

data/lib/bioroebe/toplevel_methods/taxonomy.rb CHANGED Viewed

@@ -141,8 +141,8 @@ module Taxonomy # === Bioroebe::Taxonomy
       end
     end
     if be_verbose
-      e 'Now trying to change to the base directory at '+
-        ::Bioroebe.sdir(this_dir)+'.'
+      e "Now trying to change to the base directory at "\
+        "#{::Bioroebe.sdir(this_dir)}."
     end
     cd this_dir
     e N+'We will next attempt to download the file `'+

data/lib/bioroebe/toplevel_methods/to_camelcase.rb CHANGED Viewed

@@ -11,6 +11,11 @@ module Bioroebe
   # === Bioroebe.to_camelcase
   #
   # Convert the given String (the input) into a camelcased variant.
+  #
+  # Usage example:
+  #
+  #   Bioroebe.to_camelcase('foo_bar') # => "FooBar"
+  #
   # ========================================================================= #
   def self.to_camelcase(i)
     if i.is_a? Array

data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb CHANGED Viewed

@@ -35,11 +35,6 @@ class AlignOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe
   require 'bioroebe/regexes/regexes.rb'
   require 'bioroebe/codons/codons.rb'
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
   # ========================================================================= #
   # === START_CODON
   # ========================================================================= #
@@ -67,10 +62,7 @@ class AlignOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
   # ========================================================================= #