bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb

@@ -10,16 +10,14 @@
 # =========================================================================== #
 # require 'bioroebe/conversions/convert_aminoacid_to_dna.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class ConvertAminoacidToDNA < ::Bioroebe::CommandlineApplication # === Bioroebe::ConvertAminoacidToDNA
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
+  require 'bioroebe/codons/start_codons.rb'
+  require 'bioroebe/codons/codon_table.rb'
 
   # ========================================================================= #
   # === DEFAULT_SEQUENCE
@@ -53,7 +51,7 @@ class ConvertAminoacidToDNA < ::Bioroebe::CommandlineApplication # === Bioroebe:
     # ======================================================================= #
     when :be_quiet,
          :quiet
-      @be_verbose = false
+      set_be_quiet
       run_already = true # Restore the default.
     # ======================================================================= #
     # === :do_debug
@@ -76,7 +74,7 @@ class ConvertAminoacidToDNA < ::Bioroebe::CommandlineApplication # === Bioroebe:
       # ===================================================================== #
       when :be_quiet,
            :quiet
-        @be_verbose = false
+        set_be_quiet
       end
     end
     run if run_already
@@ -87,10 +85,7 @@ class ConvertAminoacidToDNA < ::Bioroebe::CommandlineApplication # === Bioroebe:
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @start_codon_to_use
     # ======================================================================= #
@@ -130,7 +125,7 @@ class ConvertAminoacidToDNA < ::Bioroebe::CommandlineApplication # === Bioroebe:
       i = DEFAULT_SEQUENCE
     end
     if @debug
-      opnn; erev "We will work on the aminoacid sequence: `#{sfancy(i)}`"
+      opnerev "We will work on the aminoacid sequence: `#{sfancy(i)}`"
     end
     @aminoacid_sequence = i
   end; alias set_sequence set_aminoacid_sequence # === set_sequence
@@ -276,7 +271,7 @@ class ConvertAminoacidToDNA < ::Bioroebe::CommandlineApplication # === Bioroebe:
   # ========================================================================= #
   # === Bioroebe::ConvertAminoacidToDNA[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i) { :be_quiet }
   end
 

data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb

@@ -33,7 +33,7 @@
 # require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
 # Bioroebe::DnaToAminoacidSequence.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -496,11 +496,17 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     # ======================================================================= #
     ::Bioroebe.load_the_codon_table_dataset(@use_the_codon_table_for)
     _ = ensure_DNA_sequence(
-      commandline_arguments?.join(' ').strip.dup.delete(' ').delete('-') # We don't want any "-" there.
+      commandline_arguments?.join(' ').strip.dup.
+      delete(' ').
+      delete('|'). # We don't want any '|' here.
+      delete('-')  # And we don't want any "-" there either.
     )
     if _ and _.include?('.') and File.file?(_)
       _ = File.read(_).strip # Add support for reading local files here.
     end
+    if _ =~ /\d+/ # Handle input such as "5'-ATGAATAGGAAGACCTAA-3'".
+      _.delete!('[0-9]')
+    end
     # ======================================================================= #
     # Here we have to honour the correct reading frame:
     # ======================================================================= #
@@ -622,7 +628,7 @@ end # dnatoaminoacidsequence ATGATGCCTCCAGGGUAAATGCCTCCAGGGUAAGGC
 
 if __FILE__ == $PROGRAM_NAME
   alias e puts
-  require 'bioroebe/colours/rev.rb'
+  require 'bioroebe/colours/colours.rb'
   _ = ARGV
   if _.empty?
     _ = 'ATGCGTAAAGGAGAAGAACTTTTCACTTGGAGTTGTCCCAATTCTTGTTGGGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACATACGGAAAACTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCGGTTATGGTGTTCAATGCTTTGCGAGATACCCAGATCATATGAAACAGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAAAGAACTATATTTTTCAAAGATGACGGGAACTACAAGACACGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATAGAATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAATTGGAATACAACTATAACTCACACAATGTATACATCATGGCAGACAAACAAAAGAATGGAATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGAAGCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGAGAGACCACATGGTCCTTCTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGGATGAACTATACAAATAG'

data/lib/bioroebe/count/count_amount_of_aminoacids.rb

@@ -17,15 +17,12 @@
 # require 'bioroebe/count/count_amount_of_aminoacids.rb'
 # x = Bioroebe.return_composition_from_this_aminoacid_sequence('HSLOEVCKWUCKFLVNUYWYGPNRAQMDCITKM')
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class CountAmountOfAminoacids < ::Bioroebe::CommandlineApplication # === Bioroebe::CountAmountOfNucleotides 
 
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-  require 'bioroebe/toplevel_methods/atomic_composition.rb'
-
   begin
     require 'percentage'
   rescue LoadError; end
@@ -47,6 +44,7 @@ class CountAmountOfAminoacids < ::Bioroebe::CommandlineApplication # === Bioroeb
     reset
     set_string(i)
     case run_already
+    # === :use_cliner
     when :use_cliner
       @use_cliner = true
       run_already = true
@@ -57,9 +55,12 @@ class CountAmountOfAminoacids < ::Bioroebe::CommandlineApplication # === Bioroeb
     if block_given?
       yielded = yield
       case yielded
+      # ===================================================================== #
+      # === :be_quiet
+      # ===================================================================== #
       when :be_quiet,
            :be_silent
-        @be_verbose = false
+        set_be_quiet
       end
     end
     run if run_already
@@ -76,9 +77,9 @@ class CountAmountOfAminoacids < ::Bioroebe::CommandlineApplication # === Bioroeb
     @hash = {} # This Hash will keep the protein composition.
     @hash.default = 0
     # ======================================================================= #
-    # === @be_verbose
+    # === :be_verbose
     # ======================================================================= #
-    @be_verbose = true
+    set_be_verbose
   end
 
   # ========================================================================= #
@@ -141,7 +142,7 @@ class CountAmountOfAminoacids < ::Bioroebe::CommandlineApplication # === Bioroeb
     # Show the table of statistical information, in other words, how
     # many aminoacids this protein contains. This will thus show frame1.
     # ======================================================================= #
-    if @be_verbose
+    if be_verbose?
       erev "This protein (#{yellow(n_members.to_s)}#{rev} aminoacids) has "\
            "#{olivedrab('the following aminoacid composition')}#{rev} "\
            "(Frame 1)."; e
@@ -156,9 +157,9 @@ class CountAmountOfAminoacids < ::Bioroebe::CommandlineApplication # === Bioroeb
       e '  '+slateblue(key.to_s)+rev+' => '+
         yellow(value.to_s.rjust((n_aminoacids?.to_s.size)))+
         rev+' ('+sfancy(formatted_percentage_value)+rev+
-        ') ('+name_of_the_aminoacid+')' if @be_verbose
+        ') ('+name_of_the_aminoacid+')' if be_verbose?
     }
-    if @be_verbose
+    if be_verbose?
       report_how_many_aminoacids_we_have_found; e
       report_the_molecular_mass_of_these_aminoacids
       report_the_number_of_negatively_and_positively_charged_residues

data/lib/bioroebe/count/count_amount_of_nucleotides.rb

@@ -16,7 +16,7 @@
 # =========================================================================== #
 # require 'bioroebe/count/count_amount_of_nucleotides.rb
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/count/count_at.rb

@@ -36,4 +36,5 @@ if __FILE__ == $PROGRAM_NAME
   else
     p Bioroebe.count_AT(ARGV)
   end
-end # countAT ATTA
+end # countAT ATTA
+    # countAT ATTAGGGGGGG

data/lib/bioroebe/databases/download_taxonomy_database.rb

@@ -10,7 +10,7 @@
 # =========================================================================== #
 # require 'bioroebe/databases/download_taxonomy_database.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/dotplots/advanced_dotplot.rb

@@ -17,7 +17,7 @@
 # require 'bioroebe/dotplots/advanced_dotplot.rb'
 # Bioroebe::AdvancedDotplot.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -198,7 +198,7 @@ class AdvancedDotplot < ::Bioroebe::CommandlineApplication # === Bioroebe::Advan
   # ========================================================================= #
   # === Bioroebe::AdvancedDotplot.[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb

@@ -11,7 +11,7 @@
 # ============================================================================= #
 # require 'bioroebe/electron_microscopy/coordinate_analyzer.rb'
 # ============================================================================= #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -111,7 +111,7 @@ class CoordinateAnalyzer < ::Bioroebe::CommandlineApplication # === Bioroebe::El
   def report_how_many_particles_we_have_found
     n_images = @dataset.size
     unless @dataset.empty?
-      opnn; e 'We have found '+simp(@n_total_particles)+' particles in '+
+      opnerev 'We have found '+simp(@n_total_particles)+' particles in '+
               'a total of '+bold_blue(n_images.to_s)+' images.'
     end
   end

data/lib/bioroebe/electron_microscopy/fix_pos_file.rb

@@ -8,7 +8,7 @@
 # =========================================================================== #
 # 'bioroebe/fix_pos_file.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -80,7 +80,7 @@ loop_
       end
       new_file = File.dirname(@fix_this_pos_file)+
                 '/fixed_coordinates_'+File.basename(@fix_this_pos_file)
-      opnn; e 'Now storing new dataset into '+sfile(new_file)+'.'
+      opnerev 'Now storing new dataset into '+sfile(new_file)+'.'
       write_what_into(_, new_file)
     else
       opnn; no_file_exists_at(@fix_this_pos_file)

data/lib/bioroebe/electron_microscopy/flipy.rb

@@ -14,7 +14,7 @@
 # ========================================================================= #
 # require 'bioroebe/electron_microscopy/flipy.rb'
 # ========================================================================= #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -51,7 +51,7 @@ class FlipY < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicrosc
     # === --help
     # ======================================================================= #
     when /^-?-?help$/i
-      opnn; e 'Input a .mrc file.'
+      opnerev 'Input a .mrc file.'
       exit
     end
   end

data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb

@@ -8,7 +8,7 @@
 # ============================================================================= #
 # require 'bioroebe/electron_microscopy/generate_em2em_file.rb'
 # ============================================================================= #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -16,11 +16,6 @@ module ElectronMicroscopy
 
 class GenerateEm2emFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronMicroscopy::GenerateEm2emFile
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === NAME_OF_NEW_FILE
   # ========================================================================= #
@@ -54,10 +49,7 @@ class GenerateEm2emFile < ::Bioroebe::CommandlineApplication # === Bioroebe::Ele
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @name_of_new_file
     # ======================================================================= #
@@ -111,7 +103,7 @@ NAME_OPTION_SINGLE:  NAME_OF_IMPORT_FILE'
   # ========================================================================= #
   def run
     setup_dataset
-    opnn; e "Next generating file `#{sfile(@name_of_new_file)}`."
+    opnerev "Next generating file `#{sfile(@name_of_new_file)}`."
     save_dataset
   end
 

data/lib/bioroebe/electron_microscopy/parse_coordinates.rb

@@ -13,7 +13,7 @@
 # ========================================================================= #
 # require 'bioroebe/electron_microscopy/parse_coordinates.rb'
 # ========================================================================= #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -59,9 +59,9 @@ class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::Elec
     # ======================================================================= #
     @dataset = nil
     # ======================================================================= #
-    # === @be_verbose
+    # === :be_verbose
     # ======================================================================= #
-    @be_verbose = true
+    set_be_verbose
     clear_coordinates
   end
 
@@ -135,10 +135,10 @@ class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::Elec
   def report_stats
     _ = file?
     if no_file?
-      opnn; e 'No statistics can be reported because there is'
-      opnn; e 'no file at `'+sfile(_)+'`.'
+      opnerev 'No statistics can be reported because there is'
+      opnerev 'no file at `'+sfile(_)+'`.'
     else
-      opnn; e "We have #{sfancy(@array_coordinates.size.to_s)} "\
+      opnerev "We have #{sfancy(@array_coordinates.size.to_s)} "\
               "coordinates in #{sfile(_)}."
     end
   end

data/lib/bioroebe/electron_microscopy/read_file_xmd.rb

@@ -14,7 +14,7 @@
 # =========================================================================== #
 # require '/home/kumar/Robert/electron_microscopy/read_file_xmd.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -82,7 +82,7 @@ class ReadFileXMD < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronM
       @dataset = File.readlines(@this_xmd_file)
     else
       unless @this_xmd_file.empty?
-        opn; e 'The file at '+sfile(_)+' does not exist.'
+        opnerev 'The file at '+sfile(_)+rev+' does not exist.'
       end
     end
   end
@@ -134,7 +134,7 @@ class ReadFileXMD < ::Bioroebe::CommandlineApplication # === Bioroebe::ElectronM
   # ========================================================================= #
   def report_what_we_will_do
     if be_verbose?
-      opnn; e "We will next read in the data from the file #{file?}"
+      opnerev "We will next read in the data from the file #{file?}"
     end
   end
 
@@ -234,12 +234,12 @@ _rlnCoordinateY #4
   # === report                                                   (report tag)
   # ========================================================================= #
   def report
-    opnn; e 'The header subsection of this .xmd file is:'
+    opnerev 'The header subsection of this .xmd file is:'
     pp @header
     if @body
-      opnn; e 'The body subsection has '+@body.size.to_s+' entries.'
+      opnerev 'The body subsection has '+@body.size.to_s+' entries.'
     else
-      opnn; e 'No body has been found. Has a .xmd file been '\
+      opnerev 'No body has been found. Has a .xmd file been '\
               'passed to this class?'
     end
   end

data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb

@@ -14,7 +14,7 @@
 # =========================================================================== #
 # require 'bioroebe/electron_microscopy/simple_star_file_generator.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -108,7 +108,7 @@ _rlnMicrographName #1'+N
   # ========================================================================= #
   def save_dataset
     _ = save_where?
-    opnn; e "Next saving the dataset into the file `#{sfile(_)}`."
+    opnerev "Next saving the dataset into the file `#{sfile(_)}`."
     write_what_into(@_, _)
   end
 

data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb

@@ -50,4 +50,4 @@ end
 if __FILE__ == $PROGRAM_NAME
   pp Bioroebe.has_this_restriction_enzyme? 'EcoRII'  # => true
   pp Bioroebe.has_this_restriction_enzyme? 'EcoRIII' # => false  
-end
+end # ruby has_this_restriction_enzyme.rb

data/lib/bioroebe/enzymes/restriction_enzyme.rb

@@ -27,7 +27,7 @@
 # =========================================================================== #
 # require 'bioroebe/enzymes/restriction_enzyme.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb

@@ -14,7 +14,7 @@ module RestrictionEnzymes
 
 module Statistics # === Bioroebe::RestrictionEnzymes::Statistics
 
-  require 'bioroebe/constants/files_and_directories.rb'
+  require 'bioroebe/constants/constants.rb'
 
   alias e puts
 
@@ -30,7 +30,7 @@ module Statistics # === Bioroebe::RestrictionEnzymes::Statistics
   # ========================================================================= #
   def self.show
     require 'yaml'
-    require 'bioroebe/colours/rev.rb'
+    require 'bioroebe/colours/colours.rb'
     dataset = YAML.load_file(Bioroebe.file_restriction_enzymes)
     erev 'A total of '+dataset.keys.size.to_s+' restriction enzymes '\
          'are registered in this project.'
@@ -52,7 +52,8 @@ module Statistics # === Bioroebe::RestrictionEnzymes::Statistics
     e
     sorted.each {|key, value|
       erev '  Restriction size '+key.to_s.rjust(2)+' is encountered '+
-        value.to_s.rjust(3)+' times.'
+           ::Colours.lightblue(value.to_s.rjust(3))+
+           +::Bioroebe.rev+' times.'
     }
     e
   end

data/lib/bioroebe/enzymes/restriction_enzymes_file.rb

@@ -7,7 +7,7 @@
 # =========================================================================== #
 module Bioroebe
 
-  require 'bioroebe/constants/files_and_directories.rb'
+  require 'bioroebe/constants/constants.rb'
 
   # ========================================================================= #
   # === Bioroebe.restriction_enzymes_file

data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb

@@ -6,7 +6,7 @@
 # =========================================================================== #
 module Bioroebe
 
-  require 'bioroebe/colours/use_colours.rb'
+  require 'bioroebe/colours/colours.rb'
   require 'bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb'
 
   # ========================================================================= #
@@ -60,6 +60,7 @@ module Bioroebe
 end
 
 if __FILE__ == $PROGRAM_NAME
-  puts Bioroebe.return_sequence_that_is_cut_via_restriction_enzyme('EcoRI', :no_colours) # => "G|AATTC"
-  puts Bioroebe.return_sequence_that_is_cut_via_restriction_enzyme('MvnI')  
+  alias e puts
+  e Bioroebe.return_sequence_that_is_cut_via_restriction_enzyme('EcoRI', :no_colours) # => "G|AATTC"
+  e Bioroebe.return_sequence_that_is_cut_via_restriction_enzyme('MvnI')  
 end # ruby return_sequence_that_is_*.rb

data/lib/bioroebe/enzymes/show_restriction_enzymes.rb

@@ -15,11 +15,11 @@
 # require 'bioroebe/enzymes/show_restriction_enzymes.rb'
 # Bioroebe::ShowRestrictionEnzymes.new
 # =========================================================================== #
-require 'bioroebe/base/base.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
-class ShowRestrictionEnzymes < Base # === Bioroebe::ShowRestrictionEnzymes
+class ShowRestrictionEnzymes < ::Bioroebe::CommandlineApplication # === Bioroebe::ShowRestrictionEnzymes
 
   require 'bioroebe/enzymes/restriction_enzymes_file.rb'
 
@@ -97,7 +97,7 @@ class ShowRestrictionEnzymes < Base # === Bioroebe::ShowRestrictionEnzymes
   # ========================================================================= #
   # === Bioroebe::ShowRestrictionEnzymes[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/ext/main.cpp

@@ -15,7 +15,6 @@ int addition(int a, int b)
   return r;
 }
 
-
 int main(int argc, char *argv[])
 {
 

data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb

@@ -15,7 +15,7 @@
 # =========================================================================== #
 # require 'bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -58,7 +58,7 @@ class AutocorrectTheNameOfThisFastaFile < CommandlineApplication # === Bioroebe:
         new_name = new_name.split(' ').first
       end
       new_name = new_name.tr('|','_')+'.fasta'
-      opnn; erev 'Now renaming from `'+sfile(original_filename)+
+      opnerev 'Now renaming from `'+sfile(original_filename)+
                  rev+'` to `'+sfile(new_name)+'`.'
       rename(original_filename, new_name)
     else
@@ -69,7 +69,7 @@ class AutocorrectTheNameOfThisFastaFile < CommandlineApplication # === Bioroebe:
   # ========================================================================= #
   # === Bioroebe::AutocorrectTheNameOfThisFastaFile[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb

@@ -14,7 +14,7 @@
 # require 'bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb'
 # Bioroebe::CompactFastaFile.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb

@@ -14,7 +14,7 @@
 # =========================================================================== #
 # require 'bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/fasta_and_fastq/download_fasta.rb

@@ -15,7 +15,7 @@
 # =========================================================================== #
 # require 'bioroebe/fasta_and_fastq/download_fasta.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -23,11 +23,6 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
 
   require 'bioroebe/ncbi/efetch.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === BASE_URL
   # ========================================================================= #
@@ -61,16 +56,15 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #
   # === enter_log_directory
   # ========================================================================= #
-  def enter_log_directory(be_verbose = true)
+  def enter_log_directory(
+      be_verbose = true
+    )
     _ = log_dir?
     if !(return_pwd == _)
       if be_verbose
@@ -90,7 +84,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
       i = @file_is_stored_here
     )
     if i and File.exist?(i)
-      opnn; erev "The file is now stored at `#{sfile(i)}#{rev}`."
+      opnerev "The file is now stored at `#{sfile(i)}#{rev}`."
     end
   end
 
@@ -106,7 +100,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
   # ========================================================================= #
   def rename_to_fasta(i)
     @file = rds(File.dirname(i)+'/'+File.basename(i)+'.fa')
-    opnn; erev "Next renaming `#{sfile(i)}` to `#{sfile(@file)}`."
+    opnerev "Next renaming `#{sfile(i)}` to `#{sfile(@file)}`."
     mv(i, @file)
   end
 
@@ -215,7 +209,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
       if File.exist? this_file # This here is mostly done for testing-purposes.
         this_file = File.readlines(this_file).reject {|entry| entry.strip.empty? }
         unless this_file.first.include? '/'
-          opnn; erev 'Now working on '+this_file.size.to_s+' entries.'
+          opnerev 'Now working on '+this_file.size.to_s+' entries.'
           this_file.map! {|entry|
             entry = entry.dup if entry.frozen?
             entry.delete!("\n")