bioroebe 0.10.80 → 0.11.32

data/lib/bioroebe/java/bioroebe/toplevel_methods/BaseComposition.java

@@ -0,0 +1,73 @@
+/* package BaseComposition; */
+
+public class BaseComposition {
+
+  static String[] commandline_arguments;
+
+  /*
+   * Main constructor (def initialize)
+   */
+  public BaseComposition() {
+    run();
+  }
+  /*
+   * run()
+   */
+  void run() {
+    if (commandline_arguments.length == 0) {
+      en("Please provide an input argument.");
+    }
+    else {
+      String first_argument = commandline_arguments[0];
+      en(
+        "The base composition frequencies of this sequence "+
+        "(length: "+first_argument.length()+") is as follows:"
+      );
+      en("");
+      int total_length = first_argument.length();
+      int n_A = 0;
+      int n_T = 0;
+      int n_C = 0;
+      int n_G = 0;
+
+      for (int i = 0; i < total_length; i++) {
+        char this_char = first_argument.charAt(i);
+        if (this_char == 'A') {
+          n_A += 1;
+        }
+        else if (this_char == 'T') {
+          n_T += 1;
+        }
+        else if (this_char == 'C') {
+          n_C += 1;
+        }
+        else if (this_char == 'G') {
+          n_G += 1;
+        }
+      }
+      en(
+        "  A: "+Math.round((n_A * 100.0 / total_length) * Math.pow(10, 2) ) / Math.pow(10, 2)+"% "+
+        "T: "+Math.round((n_T * 100.0 / total_length) * Math.pow(10, 2) ) / Math.pow(10, 2)+"% "+
+        "C: "+Math.round((n_C * 100.0 / total_length) * Math.pow(10, 2) ) / Math.pow(10, 2)+"% "+
+        "G: "+Math.round((n_G * 100.0 / total_length) * Math.pow(10, 2) ) / Math.pow(10, 2)+"% "
+      );
+      en("");
+    }
+  }
+
+
+
+  public static void e(String i) {
+    System.out.print(i);
+  }
+
+  public static void en(String i) {
+    System.out.println(i);
+  }
+
+  public static void main(String[] args) {
+    commandline_arguments = args;
+    BaseComposition x = new BaseComposition();
+  }
+
+}

data/lib/bioroebe/misc/ruler.rb

@@ -24,6 +24,7 @@
 # variant - that one should work fine.
 # =========================================================================== #
 # require 'bioroebe/misc/ruler.rb'
+# Bioroebe.ruler_return_as_string_without_colours 'ATGCTGACAGGGGGGGEEEEEE'
 # Bioroebe::Ruler.new(ARGV)
 # =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'

data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb

@@ -27,11 +27,6 @@ class MostLikelyNucleotideSequenceForThisAminoacidSequence < ::Bioroebe::Command
   require 'bioroebe/aminoacids/codon_percentage.rb'
   require 'bioroebe/codons/possible_codons_for_this_aminoacid.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -63,10 +58,7 @@ class MostLikelyNucleotideSequenceForThisAminoacidSequence < ::Bioroebe::Command
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @internal_hash
     # ======================================================================= #

data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb

@@ -475,13 +475,6 @@ class ShowNucleotideSequence < ::Bioroebe::Sequence # === Bioroebe::ShowNucleoti
     erev i
   end; alias display report # === display (display tag)
 
-  # ========================================================================= #
-  # === do_colourize_the_start_codon
-  # ========================================================================= #
-  def do_colourize_the_start_codon
-    add_this_substring('ATG')
-  end
-
   # ========================================================================= #
   # === colourize_dna_sequence
   # ========================================================================= #
@@ -529,6 +522,13 @@ class ShowNucleotideSequence < ::Bioroebe::Sequence # === Bioroebe::ShowNucleoti
   end; alias set_search_for     search_for_this_substring # === set_search_for
        alias add_this_substring search_for_this_substring # === add_this_substring
 
+  # ========================================================================= #
+  # === do_colourize_the_start_codon
+  # ========================================================================= #
+  def do_colourize_the_start_codon
+    add_this_substring('ATG')
+  end
+
   # ========================================================================= #
   # === run
   # ========================================================================= #

data/lib/bioroebe/parsers/genbank_parser.rb

@@ -4,10 +4,29 @@
 # =========================================================================== #
 # === Bioroebe::GenbankParser
 #
-# This class can be used to parse genbank-files. Their file extension is
-# typically ".gbk".
+# This class can be used to parse genbank-files (typically stored as .genbank
+# or .gbk, so their file extension is usually ".gbk").
+#
+# Since as of the rewrite in July 2022 the class can also handle multiple
+# fasta entries now.
+#
+# The class is similar to class FastaParser, but instead it will only
+# select the content between "ORIGIN" and "VERSION" entries.
+#
+# The user can pass the content of a genbank-file to this class, and it
+# can then report the nucleotide sequence, e. g. the part starting after
+# the ORIGIN string.
+#
+# The reason why this class has been created was because it is sometimes
+# necessary to parse a genebank file.
+#
+# Usage example:
+#
+#   Bioroebe::GenbankParser.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/parsers/genbank_parser.rb'
+# require 'bioroebe/genbank/genbank_parser.rb'
+# genbank_parser = Bioroebe::GenbankParser.new(ARGV)
 # =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'
 
@@ -16,63 +35,365 @@ module Bioroebe
 class GenbankParser < ::Bioroebe::CommandlineApplication # === Bioroebe::GenbankParser
 
   # ========================================================================= #
-  # === NAMESPACE
+  # === UPCASE_THE_SEQUENCE
+  #
+  # Setting this constant to true will cause this class to store the
+  # FASTA sequence in an upcased variant, e. g. "AGCAGCTA" rather
+  # than "acgatcag".
   # ========================================================================= #
-  NAMESPACE = inspect
+  UPCASE_THE_SEQUENCE = true
+
+  # ========================================================================= #
+  # === TEST_STRING
+  #
+  # Our example test-string, to see how such a genbank file usually looks
+  # like.
+  #
+  # This will contain two different FASTA sequences.
+  # ========================================================================= #
+  TEST_STRING = '                   /note="internal transcribed spacer 2"
+ORIGIN      
+        1 cgtaacaagg tttccgtagg tgaaccttcg gaaggatcat tgttgagacc cccaaaaaaa
+       61 cgatcgagtt aatccggagg accggtgtag tttggtctcc caggggcttt ggctactgtg
+      121 gtggccgtga atttccgtcg aacctccttg ggagaattct tgatggcaat tgaacccttg
+      181 gcccggcgca gtttcgcccc aagtcaaatg agatggaacc ggcggagggc atcgtcctcc
+      241 atggaaccgg ggagggccgg cgttcttccg ttccccccat gaattttttt ttgacaactc
+      301 tcggcaacgg atatctcggc tctttgcatc cgatgaaaga acccagcgaa atgtgataag
+      361 tggtgtgaat tgcagaatcc cgtgaaccat cgagtctttg aacgcaagtt gcgcccgagg
+      421 ccatcaggct aagggcacgc ctgcctgggc gttgcgtgct gcatctctct cccattgcta
+      481 aggctgaaca ggcatactgt tcggccggcg cggatgagtg tttggcccct tgttcttcgg
+      541 tgcgatgggt ccaagacctg ggcttttgac ggccggaaat ccggcaagag gtggacggac
+      601 ggtggctgcg acgaagctgt cgtgcgaatg ccctacgctg tcgtatttga tgggccggaa
+      661 taaatccctt ttgagcccca ttggaggcac gtcaacccgt gggcggtcga cggccatttg
+      721 gatgcaaccc caggtcaggt gagga
+//
+LOCUS       Z78510                   750 bp    DNA     linear   PLN 30-NOV-2006
+DEFINITION  P.caricinum 5.8S rRNA gene and ITS1 and ITS2 DNA.
+ACCESSION   Z78510
+VERSION     Z78510.1  GI:2765635
+KEYWORDS    5.8S ribosomal RNA; 5.8S rRNA gene; internal transcribed spacer;
+            ITS1; ITS2.
+SOURCE      Phragmipedium caricinum
+  ORGANISM  Phragmipedium caricinum
+            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
+            Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;
+            Cypripedioideae; Phragmipedium.
+REFERENCE   1
+  AUTHORS   Cox,A.V., Pridgeon,A.M., Albert,V.A. and Chase,M.W.
+  TITLE     Phylogenetics of the slipper orchids (Cypripedioideae:
+            Orchidaceae): nuclear rDNA ITS sequences
+  JOURNAL   Unpublished
+REFERENCE   2  (bases 1 to 750)
+  AUTHORS   Cox,A.V.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (19-AUG-1996) Cox A.V., Royal Botanic Gardens, Kew,
+            Richmond, Surrey TW9 3AB, UK
+FEATURES             Location/Qualifiers
+     source          1..750
+                     /organism="Phragmipedium caricinum"
+                     /mol_type="genomic DNA"
+                     /db_xref="taxon:53127"
+     misc_feature    1..380
+                     /note="internal transcribed spacer 1"
+     gene            381..550
+                     /gene="5.8S rRNA"
+     rRNA            381..550
+                     /gene="5.8S rRNA"
+                     /product="5.8S ribosomal RNA"
+     misc_feature    551..750
+                     /note="internal transcribed spacer 2"
+ORIGIN      
+        1 ctaaccaggg ttccgaggtg accttcggga ggattccttt ttaagccccc gaaaaaacga
+       61 tcgaattaaa ccggaggacc ggtttaattt ggtctcccca ggggctttcc ccccttggtg
+      121 gccgtgaatt tccatcgaac ccccctggga gaattcttgg tggccaatgg acccttggcc
+      181 cggcgcaatt tcccccccaa tcaaatgaga taggaccggc agggggcgtc cccccccatg
+      241 gaaccgggga gggccggcat tcttccgttc ccccctcgga ttttttgaca actctcgcaa
+      301 cggatatctc gcctctttgc atcggatgga agaacgcagc gaaatgtgat aagtggtgtg
+      361 aattgcagaa tcccgtgaac catcgagtct ttgaacgcaa gttgcgcccg aggccatcag
+      421 gctaagggca cgcctgcctg ggcgttgcgt gctgcatctc tcccattgct aaggttgaac
+      481 gggcatactg ttcggccggc gcggatgaga gattggcccc ttgttcttcg gtgcgatggg
+      541 tccaagacct gggcttttga cggtccaaaa tccggcaaga ggtggacgga cggtggctgc
+      601 gacaaagctg tcgtgcgaat gccctgcgtt gtcgtttttg atgggccgga ataaatccct
+      661 tttgaacccc attggaggca cgtcaaccca tgggcggttg acggccattt ggatgcaacc
+      721 ccaggtcagg tgagccaccc gctgagttta
+//
+LOCUS       Z78509                   731 bp    DNA     linear   PLN 30-NOV-2006
+DEFINITION  P.pearcei 5.8S rRNA gene and ITS1 and ITS2 DNA.
+ACCESSION   Z78509
+VERSION     Z78509.1  GI:2765634
+KEYWORDS    5.8S ribosomal RNA; 5.8S rRNA gene; internal transcribed spacer;
+            ITS1; ITS2.
+SOURCE      Phragmipedium pearcei
+  ORGANISM  Phragmipedium pearcei
+            Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
+            Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;
+            Cypripedioideae; Phragmipedium.
+REFERENCE   1
+  AUTHORS   Cox,A.V., Pridgeon,A.M., Albert,V.A. and Chase,M.W.
+  TITLE     Phylogenetics of the slipper orchids (Cypripedioideae:
+            Orchidaceae): nuclear rDNA ITS sequences
+  JOURNAL   Unpublished
+REFERENCE   2  (bases 1 to 731)
+  AUTHORS   Cox,A.V.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (19-AUG-1996) Cox A.V., Royal Botanic Gardens, Kew,
+            Richmond, Surrey TW9 3AB, UK
+FEATURES             Location/Qualifiers
+     source          1..731
+                     /organism="Phragmipedium pearcei"
+                     /mol_type="genomic DNA"
+                     /db_xref="taxon:53135"
+     misc_feature    1..380
+                     /note="internal transcribed spacer 1"
+     gene            381..550
+                     /gene="5.8S rRNA"
+     rRNA            381..550
+                     /gene="5.8S rRNA"
+                     /product="5.8S ribosomal RNA"
+     misc_feature    551..731
+                     /note="internal transcribed spacer 2"
+ORIGIN      
+        1 cgtaacaagg tttccgtagg tgaacctgcg gaaggatcat tgttgagacc gccaaatata
+       61 cgatcgagtt aatccggagg accggtgtag tttggtctcc caggggcttt cgccgctgtg
+      121 gtgaccgtga tttgccatcg agcctccttg ggagatttct tgatggcaat tgaacccttg
+      181 gcccggcgca gtttcgcgcc aagtcatatg agatagaacc ggcggagggc gtcgtcctcc
+      241 atggagcggg gagggccggc atgctccgtg cccccccatg aatttttctg acaactctcg
+      301 gcaacggacg taacaaggtt taaatgtgat aagcaggtgt gaattgcaga atcccgtgaa
+      361 ccatcgagtc tttgaacgca agttgcgccc gaggccatca ggttaagggc acgcctgcct
+      421 gggcgttgcg tgctgcatct ctcccattgc taaggttgaa cgggcatact gttcggccgg
+      481 cgcggatgag agtttggccc cttgttcttc ggtgcgatgg gtccaagacc tgggcttttg
+      541 acggtccaaa atccggcaag aggtggacgg acggtggctg cgacagagct gtcgtgcgaa
+      601 tgccctacgt tgtcgttttt gatgggccag aataaatccc ttttgaaccc cattggaggc
+      661 acgtcaaccc aatggggggt gacgggcatt tggttaaccc cggcaagtta aggcacccgt
+      721 taattttagg a
+//
+LOCUS       Z78508                   741 bp    DNA     linear   PLN 30-NOV-2006'
 
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
   def initialize(
-      commandline_arguments = ARGV,
+      commandline_arguments = nil,
       run_already           = true
     )
     reset
     set_commandline_arguments(
       commandline_arguments
     )
+    menu
+    if block_given?
+      yielded = yield
+      case yielded
+      # ===================================================================== #
+      # === :do_not_report_anything
+      # ===================================================================== #
+      when :do_not_report_anything
+        @internal_hash[:report_the_dataset] = false
+      end
+    end
     run if run_already
   end
 
   # ========================================================================= #
-  # === reset
+  # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
+    # ======================================================================= #
+    # === @internal_hash
+    # ======================================================================= #
+    # @internal_hash = {}
+    # ======================================================================= #
+    # === :work_on_this_file
+    # ======================================================================= #
+    @internal_hash[:work_on_this_file] = nil
+    # ======================================================================= #
+    # === :report_the_dataset
+    # ======================================================================= #
+    @internal_hash[:report_the_dataset] = true
+    # ======================================================================= #
+    # === :n_FASTA_entries_in_the_file
+    #
+    # This variable will keep track how many FASTA entries are in
+    # the genbank file at hand.
+    # ======================================================================= #
+    @internal_hash[:n_FASTA_entries_in_the_file] = 0
+    # ======================================================================= #
+    # === :dataset_from_all_FASTA_entries_as_a_hash
+    #
+    # This hash will contain all the FASTA sequences in the given
+    # genbank file at hand. This constitutes the main dataset of
+    # this clas.
+    # ======================================================================= #
+    @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash] = {}
   end
 
   # ========================================================================= #
-  # === run
+  # === menu                                                       (menu tag)
   # ========================================================================= #
-  def run
-    _ = first_argument?
-    if _ and File.exist?(_)
-      dataset = File.readlines(_).select {|line|
-        line.start_with? '     '
-      }.map {|entry|
-        splitted = entry.strip.split(' ')
-        splitted.pop # Remove the last element.
-        splitted.join.strip
-      }
-      if dataset.is_a? Array
-        dataset = dataset.join
+  def menu(
+      i = commandline_arguments_containing_leading_hyphens?
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i # (case tag)
+      # ===================================================================== #
+      # === gparser --help
+      # ===================================================================== #
+      when /^-?-?help$/i
+        show_help
+        exit
+      # ===================================================================== #
+      # === gparser --test
+      #
+      # This entry point can be used to test the default TEST_STRING.
+      # ===================================================================== #
+      when /^-?-?test$/i,
+           /^-?-?test(-|_)?string$/i
+        analyse_this_dataset(TEST_STRING)
+        exit
       end
-      @sequence = dataset
     end
   end
 
+  # ========================================================================= #
+  # === work_on_which_file?
+  # ========================================================================= #
+  def work_on_which_file?
+    @internal_hash[:work_on_this_file]
+  end
+
+  # ========================================================================= #
+  # === report_the_dataset?
+  # ========================================================================= #
+  def report_the_dataset?
+    @internal_hash[:report_the_dataset]
+  end
+
+  # ========================================================================= #
+  # === set_work_on_this_file
+  # ========================================================================= #
+  def set_work_on_this_file(
+      i = first_argument?
+    )
+    @internal_hash[:work_on_this_file] = i
+  end
+
+  # ========================================================================= #
+  # === analyse_this_dataset
+  # ========================================================================= #
+  def analyse_this_dataset(dataset)
+    use_this_regex =
+      /ORIGIN[\/\-\.\s0-9a-zA-Z]+VERSION\s*[\.0-9A-Z]+/ # See: https://rubular.com/r/0q7rFIUflX7yzw
+    scanned = dataset.scan(use_this_regex)
+    @internal_hash[:n_FASTA_entries_in_the_file] = scanned
+    discover_the_corresponding_FASTA_entries_from_this_dataset(scanned)
+    consider_reporting_our_findings_to_the_user
+  end; alias determine_dataset analyse_this_dataset # === determine_dataset
+
+  # ========================================================================= #
+  # === dataset?
+  # ========================================================================= #
+  def dataset?
+    @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash]
+  end; alias main_dataset? dataset? # === main_dataset?
+
+  # ========================================================================= #
+  # === sequences?
+  # ========================================================================= #
+  def sequences?
+    dataset?.values
+  end
+
   # ========================================================================= #
   # === sequence?
   # ========================================================================= #
   def sequence?
-    @sequence
+    sequences?.first
   end; alias coding_sequence? sequence? # === coding_sequence?
        alias cds              sequence? # === cds
 
+  # ========================================================================= #
+  # === discover_the_corresponding_FASTA_entries_from_this_dataset
+  # ========================================================================= #
+  def discover_the_corresponding_FASTA_entries_from_this_dataset(i)
+    regex_to_use_for_the_id = /VERSION\s*([\.A-Za-z0-9]+)/
+    if i.is_a? Array
+      i.each {|this_dataset|
+        this_dataset =~ regex_to_use_for_the_id
+        use_this_id = $1.to_s.dup
+        use_this_FASTA_sequence = this_dataset.scan(
+          /^\s*\d{1,100}([\sa-zA-Z]+)/
+        ).flatten.join(' ').delete(" \n")
+        use_this_FASTA_sequence.upcase! if UPCASE_THE_SEQUENCE
+        @internal_hash[:dataset_from_all_FASTA_entries_as_a_hash][use_this_id] = use_this_FASTA_sequence
+      }
+    end
+  end
+
+  # ========================================================================= #
+  # === verbose_check_whether_the_file_exists
+  # ========================================================================= #
+  def verbose_check_whether_the_file_exists
+    _ = @internal_hash[:work_on_this_file]
+    if _ and File.exist?(_)
+      true
+    else
+      opnn; e 'No file exists at '+sfile(_)
+      false
+    end
+  end
+
+  # ========================================================================= #
+  # === consider_reporting_our_findings_to_the_user              (report tag)
+  # ========================================================================= #
+  def consider_reporting_our_findings_to_the_user
+    if report_the_dataset? and dataset? and !dataset?.empty?
+      main_dataset?.each_pair {|key, value|
+        e steelblue("#{key}:")
+        e lightblue(value)
+        e
+      }
+    end
+  end; alias report             consider_reporting_our_findings_to_the_user # === report
+       alias report_the_dataset consider_reporting_our_findings_to_the_user # === report_the_dataset
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    set_work_on_this_file(first_argument?)
+    # ======================================================================= #
+    # First check whether the given file exists or not:
+    # ======================================================================= #
+    if verbose_check_whether_the_file_exists
+      original_dataset = File.read(@internal_hash[:work_on_this_file]) # Just store it completely.
+      if original_dataset.include?('ORIGIN') and original_dataset.include?('VERSION ')
+        analyse_this_dataset(original_dataset)
+      else
+        opnn; e 'No keywords ORIGIN and VERSION were found in this file.'
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GenbankParser[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
 end; end
 
 if __FILE__ == $PROGRAM_NAME
-  _ = Bioroebe::GenbankParser.new(ARGV)
-  pp _.id
-  pp _.sequence?
-end # genbankparser *genbank
+  alias e puts
+  genbank_parser = Bioroebe::GenbankParser.new(ARGV)
+  # genbank_parser = Bioroebe::GenbankParser.new('/home/Temp/bioroebe/ls_orchid.gbk')
+  e genbank_parser.sequence?
+  # e _.id
+end # genbankparser *genbank
+    # genbankparser
+    # genbankparser sample_file.genbank
+    # genbankparser --test

data/lib/bioroebe/parsers/gff.rb

@@ -68,11 +68,6 @@ module Parser
 
 class GFF < ::Bioroebe::CommandlineApplication # === Bioroebe::Parser::GFF
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === INPUT_FILE
   #
@@ -112,10 +107,7 @@ class GFF < ::Bioroebe::CommandlineApplication # === Bioroebe::Parser::GFF
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @input_file
     # ======================================================================= #

data/lib/bioroebe/patterns/scan_for_repeat.rb

@@ -19,11 +19,6 @@ module Bioroebe
 
 class ScanForRepeat < ::Bioroebe::CommandlineApplication # === Bioroebe::ScanForRepeat
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -63,6 +58,7 @@ class ScanForRepeat < ::Bioroebe::CommandlineApplication # === Bioroebe::ScanFor
   # ========================================================================= #
   def reset
     super()
+    infer_the_namespace
     # ======================================================================= #
     # === @n_repeats
     # ======================================================================= #

data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb

@@ -21,11 +21,6 @@ class FetchFastaSequenceFromPdb < ::Bioroebe::CommandlineApplication # === Bioro
 
   require 'open-uri'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === URL_FOR_FASTA_ENTRIES_AT_THE_PDB
   # ========================================================================= #
@@ -59,10 +54,7 @@ class FetchFastaSequenceFromPdb < ::Bioroebe::CommandlineApplication # === Bioro
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @result
     # ======================================================================= #

data/lib/bioroebe/pdb/parse_mmCIF_file.rb

@@ -13,11 +13,6 @@ module Bioroebe
 
 class ParsemmCIFFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ParsemmCIFFile
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -44,10 +39,7 @@ class ParsemmCIFFile < ::Bioroebe::CommandlineApplication # === Bioroebe::Parsem
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/pdb/parse_pdb_file.rb

@@ -114,11 +114,6 @@ module Bioroebe
 
 class ParsePdbFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ParsePdbFile
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === DEFAULT_PDB_FILE
   # ========================================================================= #
@@ -171,10 +166,7 @@ class ParsePdbFile < ::Bioroebe::CommandlineApplication # === Bioroebe::ParsePdb
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @do_create_a_fasta_file
     #