bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/palindromes/palindrome_2D_structure.rb

@@ -12,7 +12,7 @@
 # require 'bioroebe/palindromes/palindrome_2D_structure.rb'
 # Bioroebe::Palindrome2DStructure.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/palindromes/palindrome_finder.rb

@@ -11,7 +11,7 @@
 # =========================================================================== #
 # require 'bioroebe/palindromes/palindrome_finder.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/palindromes/palindrome_generator.rb

@@ -16,17 +16,12 @@
 # require 'bioroebe/palindromes/palindrome_generator.rb'
 # Bioroebe.palindrome(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class PalindromeGenerator < ::Bioroebe::CommandlineApplication # === Bioroebe::PalindromeGenerator
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -56,10 +51,7 @@ class PalindromeGenerator < ::Bioroebe::CommandlineApplication # === Bioroebe::P
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @use_header_with_numbers
     #

data/lib/bioroebe/parsers/biolang_parser.rb

@@ -8,7 +8,7 @@
 # =========================================================================== #
 # require 'bioroebe/parsers/biolang_parser.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/parsers/blosum_parser.rb

@@ -14,22 +14,12 @@
 # require 'bioroebe/parsers/blosum_parser.rb'
 # Bioroebe::BlosumParser.show_as_2D_table(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class BlosumParser < ::Bioroebe::CommandlineApplication # === Bioroebe::BlosumParser
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
-  # ========================================================================= #
-  # === N
-  # ========================================================================= #
-  N = "\n"
-
   # ========================================================================= #
   # === VERTICAL_LINE
   # ========================================================================= #
@@ -52,7 +42,7 @@ class BlosumParser < ::Bioroebe::CommandlineApplication # === Bioroebe::BlosumPa
       # === :be_quiet
       # ===================================================================== #
       when :be_quiet
-        @be_verbose = false
+        set_be_quiet
       end
     end
     run if run_already
@@ -63,6 +53,7 @@ class BlosumParser < ::Bioroebe::CommandlineApplication # === Bioroebe::BlosumPa
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
     # ======================================================================= #
     # === @hash
     # ======================================================================= #
@@ -80,7 +71,7 @@ class BlosumParser < ::Bioroebe::CommandlineApplication # === Bioroebe::BlosumPa
     if i.is_a? Symbol
       i = i.to_s
     end
-    if i.include? '-'
+    if i and i.include?('-')
       i.delete!('-')
     end
     if i.is_a?(String)
@@ -125,10 +116,14 @@ class BlosumParser < ::Bioroebe::CommandlineApplication # === Bioroebe::BlosumPa
   #
   # This method can be used to store the main @hash into a yaml file.
   # ========================================================================= #
-  def save_into_a_yaml_file
+  def save_into_a_yaml_file(
+      blosum_file_to_use = @blosum_file_to_use
+    )
     what = YAML.dump(@hash)
-    into = log_dir?+File.basename(@blosum_file_to_use)
-    erev "Storing into the file `#{sfile(into)}`."
+    into = log_dir?+File.basename(blosum_file_to_use)
+    erev "Storing the (expanded) hash from the blosum file at"
+    erev "#{sfile(blosum_file_to_use)}"
+    erev "into the file #{sfile(into)}`."
     write_what_into(what, into)
   end
 
@@ -214,9 +209,9 @@ end; end
 
 if __FILE__ == $PROGRAM_NAME
   _ = Bioroebe::BlosumParser.new(ARGV)
-  pp _
+  # pp _
   _.save_into_a_yaml_file
   # Bioroebe::BlosumParser.show_as_2D_table
 end # blosumparser $BIOROEBE_YAML/blosum/blosum45.yml
-    # blosumparser blosum50
-    # blosumparser blosum62
+    # blosumparser blosum62
+    # blosumparser blosum50

data/lib/bioroebe/parsers/genbank_parser.rb

@@ -28,7 +28,7 @@
 # require 'bioroebe/genbank/genbank_parser.rb'
 # genbank_parser = Bioroebe::GenbankParser.new(ARGV)
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -201,10 +201,6 @@ LOCUS       Z78508                   741 bp    DNA     linear   PLN 30-NOV-2006'
     super()
     infer_the_namespace
     # ======================================================================= #
-    # === @internal_hash
-    # ======================================================================= #
-    # @internal_hash = {}
-    # ======================================================================= #
     # === :work_on_this_file
     # ======================================================================= #
     @internal_hash[:work_on_this_file] = nil
@@ -381,7 +377,7 @@ LOCUS       Z78508                   741 bp    DNA     linear   PLN 30-NOV-2006'
   # ========================================================================= #
   # === Bioroebe::GenbankParser[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/parsers/gff.rb

@@ -60,7 +60,7 @@
 # =========================================================================== #
 # require 'bioroebe/parsers/gff.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -214,9 +214,9 @@ class GFF < ::Bioroebe::CommandlineApplication # === Bioroebe::Parser::GFF
       # ===================================================================== #
       @array_unique_accession_ids.each {|this_accession_id|
         into = this_accession_id+'.gff3'
-        opnn; erev 'Storing dataset for the accession id '+
-                   sfancy(this_accession_id)+
-                   rev+' into the file `'+sfile(into)+'`.'
+        opnerev 'Storing dataset for the accession id '+
+                 sfancy(this_accession_id)+
+                 rev+' into the file `'+sfile(into)+'`.'
         what = @dataset.select {|line|
           line.include? this_accession_id
         }.join(N)
@@ -224,9 +224,9 @@ class GFF < ::Bioroebe::CommandlineApplication # === Bioroebe::Parser::GFF
       }
     else
       unless @input_file.nil?
-        opnn; erev 'We were instructed to split into standalone files, but we'
-        opnn; erev 'can not do so, as there is not more than one accession id'
-        opnn; erev 'in this file.'
+        opnerev 'We were instructed to split into standalone files, but we'
+        opnerev 'can not do so, as there is not more than one accession id'
+        opnerev 'in this file.'
       end 
     end
   end
@@ -240,7 +240,7 @@ class GFF < ::Bioroebe::CommandlineApplication # === Bioroebe::Parser::GFF
     if i.is_a? Array
       i.each {|entry| report_accession_id(entry) }
     else
-      opnn; erev "The accession id is `#{sfancy(i.to_s)}#{rev}`."
+      opnerev "The accession id is `#{sfancy(i.to_s)}#{rev}`."
     end
   end; alias report_this_accession_id report_accession_id # === report_this_accession_id
        alias report_all_accession_ids report_accession_id # === report_all_accession_ids
@@ -257,7 +257,7 @@ class GFF < ::Bioroebe::CommandlineApplication # === Bioroebe::Parser::GFF
       @original_dataset = File.read(_) # Read in the dataset.
       work_on_non_comments_in_that_file
     else
-      opnn; erev "The input file does not exist at #{sfancy(_)}#{rev}."
+      opnerev "The input file does not exist at #{sfancy(_)}#{rev}."
     end
   end
 

data/lib/bioroebe/parsers/parse_embl.rb

@@ -8,17 +8,12 @@
 # =========================================================================== #
 # require 'bioroebe/parsers/parse_embl.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class ParseEMBL < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseEMBL
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -38,6 +33,7 @@ class ParseEMBL < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseEMBL
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/parsers/stride_parser.rb

@@ -12,17 +12,12 @@
 #   http://webclu.bio.wzw.tum.de/stride/
 #
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
 class StrideParser < ::Bioroebe::CommandlineApplication # === Bioroebe::StrideParser
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= # 
@@ -39,10 +34,7 @@ class StrideParser < ::Bioroebe::CommandlineApplication # === Bioroebe::StridePa
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @dataset
     # ======================================================================= #
@@ -98,8 +90,8 @@ class StrideParser < ::Bioroebe::CommandlineApplication # === Bioroebe::StridePa
   # === report_result
   # ========================================================================= #
   def report_result
-    opnn; erev "The total surface area is: "\
-               "#{simp(tot_surf_area?.to_s)}"
+    opnerev "The total surface area is: "\
+            "#{simp(tot_surf_area?.to_s)}"
   end; alias report report_result # === report
 
   # ========================================================================= #

data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb

@@ -13,7 +13,7 @@
 # =========================================================================== #
 # require 'bioroebe/pattern/analyse_glycosylation_pattern.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -138,7 +138,7 @@ class AnalyseGlycosylationPattern < ::Bioroebe::CommandlineApplication # === Bio
   # ========================================================================= #
   # === Bioroebe::AnalyseGlycosylationPattern[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb

@@ -6,7 +6,7 @@
 # =========================================================================== #
 module Bioroebe
 
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
 
   # =========================================================================== #
   # === Bioroebe.is_this_sequence_a_EGF2_pattern?
@@ -42,6 +42,9 @@ module Bioroebe
       end
     end
     case use_this_pattern
+    # ======================================================================= #
+    # === :default
+    # ======================================================================= #
     when :default
       use_this_pattern = 'C-x-C-x(2)-[GP]-[FYW]-x(4,8)-C'
     end
@@ -61,6 +64,6 @@ end
 
 if __FILE__ == $PROGRAM_NAME
   puts Bioroebe.is_this_sequence_a_EGF2_pattern?(ARGV)
-end # EGF2pattern GKCDCPPGFGGDDCAE
-    # EGF2pattern XXCXCXXGFXXXXCXX
+end # EGF2pattern GKCDCPPGFGGDDCAE # true
+    # EGF2pattern XXCXCXXGFXXXXCXX # false
     # EGF2pattern XXCXCXXQFXXXXCXX

data/lib/bioroebe/patterns/profile_pattern.rb

@@ -15,7 +15,7 @@
 # =========================================================================== #
 # require 'profile_pattern.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -169,7 +169,7 @@ class ProfilePattern < ::Bioroebe::CommandlineApplication # === Bioroebe::Profil
   # ========================================================================= #
   # === Bioroebe::ProfilePattern[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/patterns/rgg_scanner.rb

@@ -18,7 +18,7 @@
 # =========================================================================== #
 # require 'bioroebe/pattern/rgg_scanner.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -62,7 +62,9 @@ class RGG_Scanner < ::Bioroebe::CommandlineApplication # === Bioroebe::RGG_Scann
   # ========================================================================= #
   # === report
   # ========================================================================= #
-  def report(array = @result)
+  def report(
+      array = @result
+    )
     sequence = sequence?
     if array.empty?
       e 'No result for '+orange('RGG')+' has been found.'

data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/alpha_helix.rb

@@ -16,9 +16,9 @@
 # A full turn takes 3.6 Aminoacids in an alpha-helix. This will be the
 # basis upon which to do calculations.
 # =========================================================================== #
-# require 'bioroebe/alpha_helix.rb'
+# require 'bioroebe/pdb_and_protein_structure/alpha_helix.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/{pdb → pdb_and_protein_structure}/download_this_pdb.rb

@@ -2,13 +2,12 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# require 'bioroebe/pdb/download_this_pdb.rb'
+# require 'bioroebe/pdb_and_protein_structure/download_this_pdb.rb'
 # Bioroebe.download_this_pdb(ARGV)
 # =========================================================================== #
 module Bioroebe
 
-  require 'bioroebe/toplevel_methods/e.rb'
-  require 'bioroebe/toplevel_methods/esystem.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
   require 'bioroebe/colours/colours.rb'
 
   require 'open-uri'

data/lib/bioroebe/{pdb → pdb_and_protein_structure}/fetch_fasta_sequence_from_pdb.rb

@@ -11,9 +11,9 @@
 #   Bioroebe::FetchFastaSequenceFromPdb.new(ARGV)
 #
 # =========================================================================== #
-# require 'bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb'
+# require 'bioroebe/pdb_and_protein_structure/fetch_fasta_sequence_from_pdb.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -103,7 +103,7 @@ class FetchFastaSequenceFromPdb < ::Bioroebe::CommandlineApplication # === Bioro
   # === run                                                         (run tag)
   # ========================================================================= #
   def run
-    @commandline_arguments.each {|this_file|
+    commandline_arguments?.each {|this_file|
       set_search_for_this_file(this_file)
       if File.exist? this_file
         data_from_the_remote_webpage = File.read(this_file)
@@ -138,7 +138,7 @@ end
 #
 # =========================================================================== #
 def self.return_fasta_sequence_from_this_pdb_file(i = ARGV)
-  require 'bioroebe/pdb/parse_pdb_file.rb'
+  require 'bioroebe/pdb_and_protein_structure/parse_pdb_file.rb'
   sequence = Bioroebe::FetchFastaSequenceFromPdb.new(i) { :be_silent }.aminoacid_sequence?
   if sequence.start_with? '>'
     sequence = sequence.split("\n")[1..-1]

data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/helical_wheel.rb

@@ -18,9 +18,9 @@
 #   echo 20DVAGHGQDILIRLFKSH  | ruby_helical_wheel > output.ps
 #
 # =========================================================================== #
-# require 'helix_wheel'
+# require 'bioroebe/pdb_and_protein_structure/helix_wheel.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_mmCIF_file.rb

@@ -7,7 +7,7 @@
 # This class shall eventually be able to parse .cif files. Currently it
 # does not work - I need to test it on a real dataset.
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 

data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_pdb_file.rb

@@ -105,10 +105,10 @@
 #   https://zhanglab.ccmb.med.umich.edu/SSIPe/pdb_atom_format.html#ATOM
 #
 # =========================================================================== #
-# require 'bioroebe/pdb/parse_pdb_file.rb'
+# require 'bioroebe/pdb_and_protein_structure/parse_pdb_file.rb'
 # Bioroebe.return_aminoacid_sequence_from_this_pdb_file
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -743,7 +743,7 @@ class ParsePdbFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ParsePdb
         analyze_the_dataset
         consider_creating_a_fasta_file
       else
-        opnn; erev "No file at `#{sfile(file)}#{rev}` could be found."
+        opnerev "No file at `#{sfile(file)}#{rev}` could be found."
         @does_the_file_exist = false
       end
     }

data/lib/bioroebe/{pdb → pdb_and_protein_structure}/report_secondary_structures_from_this_pdb_file.rb

@@ -11,9 +11,9 @@
 #   Bioroebe::ReportSecondaryStructuresFromThisPdbFile.new(ARGV)
 #
 # =========================================================================== #
-# require 'bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb'
+# require 'bioroebe/pdb_and_protein_structures/report_secondary_structures_from_this_pdb_file.rb'
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+require 'bioroebe/requires/commandline_application.rb'
 
 module Bioroebe
 
@@ -213,7 +213,7 @@ class ReportSecondaryStructuresFromThisPdbFile < ::Bioroebe::CommandlineApplicat
   # ========================================================================= #
   # === Bioroebe::ReportSecondaryStructuresFromThisPdbFile[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 

data/lib/bioroebe/project/project.rb

@@ -117,9 +117,11 @@ CODON_TABLES_DIRECTORY_FREQUENCY =
 
 # =========================================================================== #
 # === PDB_DIRECTORY
+#
+# This is called pdb_and_protein_structure/ since as of November 2023.
 # =========================================================================== #
 PDB_DIRECTORY =
-  "#{@project_base_directory}pdb/"
+  "#{@project_base_directory}pdb_and_protein_structure/"
 
 # =========================================================================== #
 # === PARSERS_DIRECTORY

data/lib/bioroebe/raw_sequence/README.md

@@ -6,12 +6,12 @@ Specifically it does NOT contain any colour-related code or
 output-related methods, so "alias e puts" can NOT be found
 in a RawSequence.
 
-The reason this class was added in 2021 was because there 
-were some bugs in the Bioroebe::Sequence, which in particular
-caused the bioshell interface to show odd formatting results
-on the commandline.
+The reason this class was added in the year 2021 was because
+there were some bugs in the Bioroebe::Sequence, which in
+particular caused the bioshell interface to show odd formatting
+ results on the commandline.
 
-RawSequence bypasses this issue completely, by being much,
-much simpler than Bioroebe::Sequence. Internally
-Bioroebe::Sequence will rely on RawSequence for sequence
-data.
+RawSequence bypasses this issue completely, by being much, much 
+simpler than Bioroebe::Sequence. Internally Bioroebe::Sequence
+will rely on RawSequence for sequence data, so this is a basic
+building block.

data/lib/bioroebe/raw_sequence/raw_sequence.rb

@@ -4,6 +4,8 @@
 # =========================================================================== #
 # === Bioroebe::RawSequence
 #
+# This is the base class for any sequence object.
+#
 # Usage example:
 #
 #   Bioroebe::RawSequence.new(ARGV)
@@ -539,7 +541,8 @@ if __FILE__ == $PROGRAM_NAME
   # Next comes some testing code.
   # ========================================================================= #
   require 'cliner/autoinclude'
-  alias e puts
+  alias e  puts
+  alias ee print
   cliner
   x = Bioroebe::RawSequence.new('ATGGATCGATGC')
   y = Bioroebe::RawSequence.new('TTTGATCGATGC')
@@ -553,5 +556,11 @@ if __FILE__ == $PROGRAM_NAME
   pp raw_sequence.composition?
   raw_sequence.first_position = 'T'
   pp raw_sequence.composition?
-  puts raw_sequence.start_end(1, 3)
+  e raw_sequence.start_end(1, 3)
+  e
+  e 'Composition of ATGCATTTT:'
+  e
+  seq = Bioroebe::RawSequence.new("ATGCATTTT")
+  ee '  '; pp seq.composition # => {"A"=>2, "T"=>5, "G"=>1, "C"=>1}
+  e
 end # rawsequence ATGC

data/lib/bioroebe/regexes/regexes.rb

@@ -6,8 +6,6 @@
 # =========================================================================== #
 module Bioroebe
 
-  require 'bioroebe/codons/start_codons.rb'
-
   # ========================================================================= #
   # === Bioroebe.regex_with_startcodons
   #
@@ -21,6 +19,7 @@ module Bioroebe
   def self.regex_with_startcodons(
       use_this_start_codon = ::Bioroebe.start_codon?
     )
+    require 'bioroebe/codons/start_codons.rb'
     start_codon_as_mRNA = use_this_start_codon.
                           tr('T','U') 
     regex = /(#{use_this_start_codon}|#{start_codon_as_mRNA})/i

data/lib/bioroebe/requires/commandline_application.rb

@@ -2,4 +2,6 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-require 'bioroebe/base/commandline_application/commandline_application.rb'
+# require 'bioroebe/requires/commandline_application.rb'
+# =========================================================================== #
+require 'bioroebe/base/commandline_application/commandline_application.rb'

data/lib/bioroebe/requires/require_all_pdb_files.rb

@@ -16,7 +16,7 @@ module Bioroebe
     )
     _ = Dir["#{pdb_dir}*.rb"]
     _.each {|file|
-      file = "bioroebe/pdb/#{File.basename(file)}"
+      file = "bioroebe/pdb_and_protein_structure/#{File.basename(file)}"
       require file
     }
   end

data/lib/bioroebe/requires/require_all_taxonomy_files.rb

@@ -14,7 +14,7 @@ module Bioroebe
   # === Bioroebe.taxonomy_directory?
   # ========================================================================= #
   def self.taxonomy_directory?
-    "#{::Bioroebe.project_base_dir?}taxonomy/"
+    "#{project_base_dir?}taxonomy/"
   end
 
   # ========================================================================= #

data/lib/bioroebe/requires/require_all_utility_scripts_files.rb

@@ -25,6 +25,16 @@ module Bioroebe
     require 'bioroebe/utility_scripts/compseq/compseq.rb'
     require 'bioroebe/utility_scripts/showorf/showorf.rb'
     require 'bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb'
+    require 'bioroebe/utility_scripts/pathways/pathways.rb'
+    require 'bioroebe/utility_scripts/download_files_from_rebase/download_files_from_rebase.rb'
+    require 'bioroebe/utility_scripts/punnet/punnet.rb'
+    require 'bioroebe/utility_scripts/permutations/permutations.rb'
+    require 'bioroebe/utility_scripts/mirror_repeat/mirror_repeat.rb'
+    require 'bioroebe/utility_scripts/parse_taxonomy/parse_taxonomy.rb'
+    require 'bioroebe/utility_scripts/consensus_sequence/consensus_sequence.rb'
+    require 'bioroebe/utility_scripts/show_this_dna_sequence/show_this_dna_sequence.rb'
+    require 'bioroebe/utility_scripts/create_batch_entrez_file/create_batch_entrez_file.rb'
+    require 'bioroebe/utility_scripts/fetch_data_from_uniprot/fetch_data_from_uniprot.rb'
   end
 
   require_all_utility_scripts_files # Call it at once.