bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb

@@ -26,7 +26,7 @@
 # require 'bioroebe/utility_scripts/align_open_reading_frames.rb'
 # Bioroebe::AlignOpenReadingFrames.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -34,6 +34,7 @@ class AlignOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe
 
   require 'bioroebe/regexes/regexes.rb'
   require 'bioroebe/codons/codons.rb'
+  require 'bioroebe/codons/start_codons.rb'
 
   # ========================================================================= #
   # === START_CODON
@@ -150,8 +151,8 @@ class AlignOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe
   # ========================================================================= #
   def report_that_no_ORF_has_been_found
     this_length = input?.size
-    opnn; erev "No valid stop-codon has been found for the given input"
-    opnn; erev "sequence of length #{sfancy(this_length.to_s)}."
+    opnerev "No valid stop-codon has been found for the given input"
+    opnerev "sequence of length #{sfancy(this_length.to_s)}."
   end
 
   # ========================================================================= #

data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb

@@ -15,7 +15,7 @@
 # require 'bioroebe/utility_scripts/analyse_local_dataset.rb'
 # Bioroebe::AnalyseLocalDataset.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -108,7 +108,7 @@ class AnalyseLocalDataset < ::Bioroebe::CommandlineApplication # === Bioroebe::A
   # ========================================================================= #
   # === Bioroebe::AnalyseLocalDataset[]
   # ========================================================================= #
-  def self.[](i)
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb

@@ -13,7 +13,7 @@
 # =========================================================================== #
 # require 'bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -88,9 +88,9 @@ class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::Ch
   # This method is to fetch user input.
   # ========================================================================= #
   def get_user_input
-    opnn; erev 'Input your first sequence now:'
+    opnerev 'Input your first sequence now:'
     first_sequence = $stdin.gets.chomp
-    opnn; erev 'Input your second sequence now:'
+    opnerev 'Input your second sequence now:'
     second_sequence = $stdin.gets.chomp
     set_data(first_sequence, second_sequence)
   end
@@ -103,11 +103,18 @@ class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::Ch
       result = corresponding_nucleotide(@second_sequence[index])
       if character == result # then all is fine
       else # else this is not fine so we spit out the problem.
-        @array_mismatches << [index+1, character]
+        array_mismatches? << [index+1, character]
       end
     }
   end
 
+  # ========================================================================= #
+  # === array_mismatches?
+  # ========================================================================= #
+  def array_mismatches?
+    @array_mismatches
+  end
+
   # ========================================================================= #
   # === corresponding_nucleotide
   # ========================================================================= #
@@ -157,14 +164,14 @@ class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::Ch
   # === report_results                                           (report tag)
   # ========================================================================= #
   def report_results
-    mismatches = @array_mismatches
+    mismatches = array_mismatches?
     if mismatches.empty?
       e
       erev 'We found no mismatch.'
       e
     else
       e
-      erev 'We found '+swarn('mismatches ')+rev+'at:'
+      erev swarn('Mismatches')+rev+' were found at the following locations:'
       e
       first_sequence  = @first_sequence
       second_sequence = @second_sequence
@@ -175,7 +182,7 @@ class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::Ch
           ', Nucleotide being: '+sfancy(character.to_s)
       }
       e
-      @array_mismatches.reverse.each {|index, character|
+      array_mismatches?.reverse.each {|index, character|
         colourized_first_sequence[index-1,1]  = send(COLOUR_TO_BE_USED_FOR_A_MISMATCH, character)+
                                                 rev
         corresponding_character = colourized_second_sequence[index-1,1]
@@ -209,8 +216,8 @@ class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::Ch
   # ========================================================================= #
   def run
     get_user_input if @obtain_user_input
-    opnn; e rev+'We will now compare these two sequences'
-    opnn; e rev+'for any potential mismatch(es).'
+    opnerev 'We will now compare these two sequences'
+    opnerev 'for any potential mismatch(es).'
     scan_for_mismatches
     report_results
   end

data/lib/bioroebe/utility_scripts/compacter/compacter.rb

@@ -15,7 +15,7 @@
 # =========================================================================== #
 # require 'bioroebe/utility_scripts/compacter/compacter.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -97,6 +97,7 @@ class Compacter < ::Bioroebe::CommandlineApplication # === Bioroebe::Compacter
       # Usage example:
       #
       #   compacter SPRR4_protein.fasta --retain-newlines
+      #   compacter *eukin*.fasta --retain-newlines
       #
       # ===================================================================== #
       when /-?-?retain(-|_)?newlines/
@@ -117,7 +118,8 @@ class Compacter < ::Bioroebe::CommandlineApplication # === Bioroebe::Compacter
   # === show_help (help tag)
   # ========================================================================= #
   def show_help
-    opnn { :no_newline }
+    opnn { :no_trailing }
+    e
     e
     e '  --retain-newlines # retain newlines, aka do not dump into a single line'
     e

data/lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb

@@ -0,0 +1,119 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::CompareTheseTwoSequencesViaBlosum
+#
+# This class can be used to compare to sequences, towards a blosum file,
+# such as BLOSUM50, and print out the score.
+#
+# Usage examples:
+#
+#   Bioroebe::CompareTheseTwoSequencesViaBlosum.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb'
+# Bioroebe::CompareTheseTwoSequencesViaBlosum.new(ARGV)
+# =========================================================================== #
+require 'bioroebe/requires/commandline_application.rb'
+
+module Bioroebe
+
+class CompareTheseTwoSequencesViaBlosum < ::Bioroebe::CommandlineApplication # === Bioroebe::CompareTheseTwoSequencesViaBlosum
+
+  # ========================================================================= #
+  # === USE_THIS_FILE
+  # ========================================================================= #
+  USE_THIS_FILE = '/home/x/Temp/bioroebe/blosum50.yml'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      i           = nil,
+      run_already = true
+    )
+    reset
+    set_commandline_arguments(i)
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super()
+    # ======================================================================= #
+    # === :dataset
+    # ======================================================================= #
+    @internal_hash[:dataset] = YAML.load_file(USE_THIS_FILE)
+    set_be_quiet # Or set_be_verbose
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    _ = commandline_arguments?
+    sequence1 = _[0]
+    sequence2 = _[1]
+    do_work_through_these_two_sequences(sequence1, sequence2)
+  end
+
+  # ========================================================================= #
+  # === do_work_through_these_two_sequences
+  # ========================================================================= #
+  def do_work_through_these_two_sequences(a, b)
+    dataset = @internal_hash[:dataset]
+    b_chars = b.chars
+    total_score = 0
+    gap_is_open = false
+    be_verbose = be_verbose?
+    a.chars.each_with_index {|char, index|
+      char1 = char
+      char2 = b_chars[index]
+      if char1 == '-' or char2 == '-'
+        if gap_is_open
+          total_score += (-2)
+          if be_verbose
+            erev 'Gap extension cost for the two elements '+char1+char2+
+              ' total score is now: '+tomato(total_score.to_s)+rev+')'
+          end
+        else
+          total_score += (-12)
+          if be_verbose
+            erev 'Gap open cost for the two elements '+char1+char2+
+              ' total score is now: '+tomato(total_score.to_s)+rev+')'
+          end
+        end
+        gap_is_open = true
+      else
+        gap_is_open = false # Always close it then.
+        value = dataset[char1 + char2]
+        total_score += value
+        if be_verbose
+          erev 'Normal BLOSUM50 cost for the two elements '+
+            char1+char2+' '+
+            tomato(
+              '(add '+value.to_s+
+              ' total score is now: '+total_score.to_s+')'
+            )+rev
+        end
+        
+      end
+    }
+    erev 'The final score of these two sequences is '+royalblue(total_score)+rev+'.'
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::CompareTheseTwoSequencesViaBlosum[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::CompareTheseTwoSequencesViaBlosum.new(ARGV)
+end # comparethesetwosequencesviablosum GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD----LHAHK GSGYLVGDSLTFVDLL--VAQHTADLLAANAALLDEFPQFKAHQ

data/lib/bioroebe/utility_scripts/compseq/compseq.rb

@@ -28,7 +28,7 @@
 # require 'bioroebe/utility_scripts/compseq/compseq.rb'
 # Bioroebe::Compseq.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -105,9 +105,9 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
     super()
     infer_the_namespace
     # ======================================================================= #
-    # === @identifier
+    # === @internal_hash[:identifier]
     # ======================================================================= #
-    @identifier = nil
+    @internal_hash[:identifier] = nil
     # ======================================================================= #
     # === @hash
     # ======================================================================= #
@@ -124,7 +124,7 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
   def set_word_size(
       i = DEFAULT_WORD_SIZE
     )
-    @word_size = i
+    @internal_hash[:word_size] = i
   end
 
   # ========================================================================= #
@@ -140,8 +140,8 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
     # === Handle empty input given next
     # ======================================================================= #
     if i.empty?
-      opnn; erev 'Please provide an input, either an existing file, or the'
-      opnn; erev 'raw FASTA sequence embedded in "" quotes, for instance.'
+      opnerev 'Please provide an input, either an existing file, or the'
+      opnerev 'raw FASTA sequence embedded in "" quotes, for instance.'
     end
     # ======================================================================= #
     # === Handle > FASTA identifier next
@@ -171,14 +171,16 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
   # ========================================================================= #
   def set_identifier(i)
     i =~ />gi\|\d+\|ref\|(NM.+)\|/ # http://rubular.com/r/dbx08WzdAZ
-    @identifier = $1.to_s.dup
+    @internal_hash[:identifier] = $1.to_s.dup
   end
 
   # ========================================================================= #
   # === identifier?
+  #
+  # This method must guarantee to return a String.
   # ========================================================================= #
   def identifier?
-    @identifier.to_s
+    @internal_hash[:identifier].to_s
   end
 
   # ========================================================================= #
@@ -379,7 +381,7 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
   # === word_size?
   # ========================================================================= #
   def word_size?
-    @word_size
+    @internal_hash[:word_size]
   end
 
   # ========================================================================= #

data/lib/bioroebe/utility_scripts/{consensus_sequence.rb → consensus_sequence/consensus_sequence.rb}

@@ -9,15 +9,20 @@
 # You have to input several sequences to this class - at the least
 # two.
 # =========================================================================== #
-# require 'bioroebe/utility_scripts/consensus_sequence.rb'
+# require 'bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb'
 # Bioroebe::ConsensusSequence.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::ConsensusSequence
 
+  # ========================================================================= #
+  # === A_T_or_C
+  # ========================================================================= #
+  A_T_or_C = %w( A T C )
+
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -164,12 +169,13 @@ class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::Con
     %w( A T ).sample
   end
 
-
   # ========================================================================= #
   # === return_A_or_T_or_C
+  #
+  # This method will randomly pick either A, T or C.
   # ========================================================================= #
   def return_A_or_T_or_C
-    %w( A T C ).sample
+    A_T_or_C.sample
   end
 
   # ========================================================================= #
@@ -198,6 +204,9 @@ class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::Con
       be_verbose = be_verbose?
     )
     case be_verbose
+    # ======================================================================= #
+    # === :be_verbose
+    # ======================================================================= #
     when :be_verbose
       be_verbose = true
     end

data/lib/bioroebe/utility_scripts/{create_batch_entrez_file.rb → create_batch_entrez_file/create_batch_entrez_file.rb}

@@ -14,12 +14,12 @@
 #
 # Usage example:
 #
-#   Bioroebe::CreateBatchEntrezFile.new
+#   Bioroebe::CreateBatchEntrezFile.new(ARGV)
 #
 # =========================================================================== #
-# require 'bioroebe/utility_scripts/create_batch_entrez_file.rb'
+# require 'bioroebe/utility_scripts/create_batch_entrez_file/create_batch_entrez_file.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -95,7 +95,7 @@ https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2
   # ========================================================================= #
   def store_input_into_a_file
     this_file = 'input_files.fasta'
-    opnn; e "Now storing into `#{sfile(this_file)}`."
+    opnerev "Now storing into `#{sfile(this_file)}`."
     what = @input.join(N)
     into = this_file
     write_what_into(what, into)
@@ -111,7 +111,7 @@ https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2
   # ========================================================================= #
   # === Bioroebe::CreateBatchEntrezFile[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/utility_scripts/{determine_antigenic_areas.rb → determine_antigenic_areas/determine_antigenic_areas.rb}

@@ -23,16 +23,16 @@
 #
 # Usage example:
 #
-#   Bioroebe::DetermineAntigenicAreas.new
+#   Bioroebe::DetermineAntigenicAreas.new(ARGV)
 #
 # =========================================================================== #
-# require 'bioroebe/utility_scripts/determine_antigenic_areas.rb'
+# require 'bioroebe/utility_scripts/determine_antigenic_areas/determine_antigenic_areas.rb'
 # =========================================================================== #
-require 'bioroebe/base/base.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
-class DetermineAntigenicAreas < Base # === Bioroebe::DetermineAntigenicAreas.new
+class DetermineAntigenicAreas  < ::Bioroebe::CommandlineApplication # === Bioroebe::DetermineAntigenicAreas
 
   # ========================================================================= #
   # === ARRAY_IMPORTANT_HYDROPHOBIC_RESIDUES
@@ -104,7 +104,7 @@ class DetermineAntigenicAreas < Base # === Bioroebe::DetermineAntigenicAreas.new
   # ========================================================================= #
   # === Bioroebe::DetermineAntigenicAreas[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/utility_scripts/{determine_missing_nucleotides_percentage.rb → determine_missing_nucleotides_percentage/determine_missing_nucleotides_percentage.rb}

@@ -17,7 +17,7 @@
 # =========================================================================== #
 # require 'bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -67,18 +67,10 @@ class DetermineMissingNucleotidesPercentage < ::Bioroebe::CommandlineApplication
   # === sanitize_input
   # ========================================================================= #
   def sanitize_input
-    if input?.include? ' + '
-      set_input(input?.gsub(/ \+/,''))
-    end
-    if input?.include? 'content'
-      set_input(input?.gsub(/content/,''))
-    end
-    if input?.include? 'is'
-      set_input(input?.gsub(/is/,''))
-    end
-    if input?.include? 'percent'
-      set_input(input?.gsub(/percent/,'%'))
-    end
+    set_input(input?.gsub(/ \+/,'')) if input?.include? ' + '
+    set_input(input?.gsub(/content/,'')) if input?.include? 'content'
+    set_input(input?.gsub(/is/,'')) if input?.include? 'is'
+    set_input(input?.gsub(/percent/,'%')) if input?.include? 'percent'
     @input.delete!('.')
     @input.strip!
   end
@@ -109,11 +101,20 @@ class DetermineMissingNucleotidesPercentage < ::Bioroebe::CommandlineApplication
     @hash[:c] = @percentage / 2
   end; alias determine_atcg_content determine_a_t_c_g_content # === determine_atcg_content
 
+  # ========================================================================= #
+  # === hash?
+  # ========================================================================= #
+  def hash?
+    @hash
+  end
+
   # ========================================================================= #
   # === report_atcg_content
   # ========================================================================= #
-  def report_atcg_content
-    @hash.each_pair {|key, value|
+  def report_atcg_content(
+      i = hash?
+    )
+    i.each_pair {|key, value|
       erev "#{key.to_s.upcase} has: "\
            "#{steelblue(value.to_s+'%')}#{rev}"
     }

data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb

@@ -10,19 +10,19 @@
 # require 'bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb'
 # Bioroebe::DisplayOpenReadingFrames.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
-require 'bioroebe/utility_scripts/display_open_reading_frames/determine.rb'
-require 'bioroebe/utility_scripts/display_open_reading_frames/initialize.rb'
-require 'bioroebe/utility_scripts/display_open_reading_frames/menu.rb'
-require 'bioroebe/utility_scripts/display_open_reading_frames/misc.rb'
-require 'bioroebe/utility_scripts/display_open_reading_frames/report.rb'
-require 'bioroebe/utility_scripts/display_open_reading_frames/reset.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class DisplayOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe::DisplayOpenReadingFrames
 
   require 'bioroebe/sequence/dna.rb'
+  require 'bioroebe/utility_scripts/display_open_reading_frames/determine.rb'
+  require 'bioroebe/utility_scripts/display_open_reading_frames/initialize.rb'
+  require 'bioroebe/utility_scripts/display_open_reading_frames/menu.rb'
+  require 'bioroebe/utility_scripts/display_open_reading_frames/misc.rb'
+  require 'bioroebe/utility_scripts/display_open_reading_frames/report.rb'
+  require 'bioroebe/utility_scripts/display_open_reading_frames/reset.rb'
 
 end; end
 

data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb

@@ -12,7 +12,7 @@ class DisplayOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroe
   # === set_dna_sequence
   # ========================================================================= #
   def set_dna_sequence(
-      i = @commandline_arguments.first
+      i = commandline_arguments?.first
     )
     i = i.to_s.dup # We always want a free, unfrozen sequence here.
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb

@@ -8,6 +8,8 @@ module Bioroebe
 
 class DisplayOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe::DisplayOpenReadingFrames
 
+  require 'bioroebe/codons/start_codons.rb'
+
   # ========================================================================= #
   # === show_the_intro_for_this_class
   # ========================================================================= #

data/lib/bioroebe/utility_scripts/{dot_alignment.rb → dot_alignment/dot_alignment.rb}

@@ -12,10 +12,10 @@
 #   Bioroebe::DotAlignment.new(ARGV)
 #
 # =========================================================================== #
-# require 'bioroebe/utility_scripts/dot_alignment_frames.rb'
+# require 'bioroebe/utility_scripts/dot_alignment_frames/dot_alignment_frames.rb'
 # Bioroebe::DotAlignment.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -156,7 +156,7 @@ class DotAlignment < ::Bioroebe::CommandlineApplication # === Bioroebe::DotAlign
   # ========================================================================= #
   # === Bioroebe::DotAlignment[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/utility_scripts/{download_files_from_rebase.rb → download_files_from_rebase/download_files_from_rebase.rb}

@@ -13,7 +13,7 @@
 # require 'bioroebe/utility_scripts/download_files_from_rebase.rb'
 # Bioroebe::DownloadFilesFromRebase.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -42,16 +42,16 @@ class DownloadFilesFromRebase < ::Bioroebe::CommandlineApplication # === Bioroeb
   def reset
     super()
     # ======================================================================= #
-    # === @array_download_these_remote_files
+    # === :array_download_these_remote_files
     # ======================================================================= #
-    @array_download_these_remote_files = %w( emboss_e.txt )
+    @internal_hash[:array_download_these_remote_files] = %w( emboss_e.txt )
   end
 
   # ========================================================================= #
   # === run
   # ========================================================================= #
   def run
-    @array_download_these_remote_files.each {|this_remote_file|
+    @internal_hash[:array_download_these_remote_files].each {|this_remote_file|
       _ = REMOTE_BASE_URL+this_remote_file
       erev "Now dowloading #{sfile(_)}#{rev}."
       esystem "wget #{_}"
@@ -61,7 +61,7 @@ class DownloadFilesFromRebase < ::Bioroebe::CommandlineApplication # === Bioroeb
   # ========================================================================= #
   # === Bioroebe::DownloadFilesFromRebase[]
   # ========================================================================= #
-  def self.[](i)
+  def self.[](i = ARGV)
     new(i)
   end