bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/C++/DNA.cpp

@@ -0,0 +1,69 @@
+#include <algorithm>
+#include <iostream>
+#include <string>
+#include "sequence.cpp"
+
+using namespace std;
+
+/*
+ * The idea behind this class is to represent a DNA sequence.
+ *
+ * Ideally it can be re-used across the bioroebe-suite.
+ */
+
+/*
+ * class DNA : public Sequence {}
+ *
+ */
+
+class DNA : public Sequence
+{
+
+  /*
+   * query_sequence()
+   */
+public: /* Public access members are accessible anywhere. */
+
+  DNA() /* Our default constructor */
+  {
+    /* cout << "Default constructor invoked." << endl; */
+  }
+  /*~DNA()
+  {
+    std::cout << "Object has been eliminated." << endl;
+  }*/ /* Our default destructor - presently not in use for this class. */
+  DNA(string i) /* If we want to use a String as sequence. */
+  {
+    set_sequence(i);
+  }
+
+  /*
+   * report_as_RNA()
+   */
+  void report_as_RNA() {
+    string result = query_sequence(); /* Copy the sequence here. */
+    std::replace(
+      result.begin(),
+      result.end(),
+      'T',
+      'U'
+    ); /* Replace all 'T' with 'U' */
+    cout << result << endl;
+  }
+
+};
+
+int main()
+{
+  /* This is mostly for testing: */
+  DNA dna;
+  dna.set_sequence("ATGC");
+  dna.report();
+  dna.set_sequence("TTTT");
+  dna.report();
+  dna.report_as_RNA();
+  dna.report();
+  DNA dna2("GGCC");
+  dna2.report();
+  return EXIT_SUCCESS;
+}

data/lib/bioroebe/C++/RNA.cpp

@@ -0,0 +1,58 @@
+#include <algorithm>
+#include <iostream>
+#include <string>
+#include "sequence.cpp"
+
+using namespace std; 
+
+/*
+ * The idea behind this class is to represent a RNA sequence.
+ *
+ * Ideally it can be re-used across the bioroebe-suite.
+ */
+
+class RNA : public Sequence
+{
+
+  /*
+   * query_sequence()
+   */
+public: /* Public access members are accessible anywhere. */
+
+  RNA() /* Our default constructor */
+  {
+    /* cout << "Default constructor invoked." << endl; */
+  }
+  /*~RNA()
+  {
+    std::cout << "Object has been eliminated." << endl;
+  }*/ /* Our default destructor - presently not in use for this class. */
+  RNA(string i) /* If we want to use a String as sequence. */
+  {
+    set_sequence(i);
+  }
+
+  /*
+   * report_as_RNA()
+   */
+  void report_as_RNA() {
+    string result = query_sequence(); /* Copy the sequence here. */
+    std::replace(
+      result.begin(),
+      result.end(),
+      'T',
+      'U'
+    ); /* Replace all 'T' with 'U' */
+    cout << result << endl;
+  }
+
+};
+
+int main() 
+{
+  /* This is mostly for testing: */
+  RNA rna;
+  rna.set_sequence("ATGC");
+  rna.report();
+  return EXIT_SUCCESS; 
+} 

data/lib/bioroebe/C++/sequence.cpp

@@ -0,0 +1,35 @@
+#include <iostream>
+#include <string>
+
+using namespace std;
+
+class Sequence {
+
+private: /* Simply make it more specific here. */
+
+  string sequence = ""; 
+
+public:
+
+  /*
+   * query_sequence()
+   */
+  string query_sequence() {
+    return sequence;
+  }
+
+  /*
+   * report()                                                      (report tag)
+   */
+  void report() {
+    cout << query_sequence() << endl;
+  }
+  /*
+   * set_sequence()
+   *
+   * Specify a new sequence here.
+   */
+  void set_sequence(string i) {
+    sequence = i;
+  }
+};

data/lib/bioroebe/abstract/README.md

@@ -0,0 +1 @@
+This is for testing various ideas. It won't be required normally.

data/lib/bioroebe/abstract/features.rb

@@ -0,0 +1,29 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Features
+# =========================================================================== #
+module Bioroebe
+
+module Features # === Bioroebe::Features
+
+  # ========================================================================= #
+  # === can_self_excise?
+  #
+  # RNA such as in etrahymena thermophila can cleave out 400
+  # nucleotides. For such a RNA the method must then return
+  # true.
+  # ========================================================================= #
+  def can_self_excise?
+    false
+  end
+
+  # ========================================================================= #
+  # === is_a_ribozyme?
+  # ========================================================================= #
+  def is_a_ribozyme?
+    false
+  end
+
+end; end

data/lib/bioroebe/aminoacids/aminoacid_substitution.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class AminoacidSubstitution < ::Bioroebe::CommandlineApplication # === Bioroebe::AminoacidSubstitution
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -49,10 +44,7 @@ class AminoacidSubstitution < ::Bioroebe::CommandlineApplication # === Bioroebe:
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/aminoacids/codon_percentage.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class CodonPercentage < ::Bioroebe::CommandlineApplication # === Bioroebe::CodonPercentage
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -45,10 +40,7 @@ class CodonPercentage < ::Bioroebe::CommandlineApplication # === Bioroebe::Codon
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @internal_hash
     # ======================================================================= #

data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb

@@ -38,11 +38,6 @@ class DeduceAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroeb
   require 'bioroebe/codons/possible_codons_for_this_aminoacid.rb'
   require 'bioroebe/misc/ruler.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === DEFAULT_SEQUENCE
   #
@@ -73,10 +68,7 @@ class DeduceAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroeb
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @internal_hash
     # ======================================================================= #

data/lib/bioroebe/aminoacids/display_aminoacid_table.rb

@@ -79,6 +79,7 @@ class DisplayAminoacidTable < Bioroebe::CommandlineApplication # === Bioroebe::D
     if i.is_a? Array
       i = i.join(' ').strip
     end
+    i = ::Bioroebe.filter_away_invalid_aminoacids(i)
     @input = i
   end
 

data/lib/bioroebe/aminoacids/show_hydrophobicity.rb

@@ -27,11 +27,6 @@ class ShowHydrophobicity < ::Bioroebe::CommandlineApplication # === Bioroebe::Sh
     HYDROPATHY_TABLE = YAML.load_file(FILE_HYDROPATHY_TABLE)
   end
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -142,7 +137,7 @@ class ShowHydrophobicity < ::Bioroebe::CommandlineApplication # === Bioroebe::Sh
   # ========================================================================= #
   def opnn(i = nil)
     hash = {}
-    hash.merge!(namespace: NAMESPACE)
+    hash.merge!(namespace: namespace?)
     hash.merge!(i) if i
     super(hash)
   end

data/lib/bioroebe/base/base_module/base_module.rb

@@ -0,0 +1,36 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This module will be included into both Bioroebe::Base as well as
+# Bioroebe::CommandlineApplication.
+# =========================================================================== #
+# require 'bioroebe/base/base_module/base_module.rb'
+# include Bioroebe::BaseModule
+# =========================================================================== #
+module Bioroebe
+
+module BaseModule # === Bioroebe::BaseModule
+
+  # ========================================================================= #
+  # === file_readlines
+  #
+  # This method is merely a wrapper over File.readlines().
+  # ========================================================================= #
+  def file_readlines(
+      i, encoding_to_use = main_encoding?
+    )
+    File.readlines(i, encoding: encoding_to_use)
+  end; alias readlines         file_readlines # === readlines
+       alias default_readlines file_readlines # === default_readlines
+
+  # ========================================================================= #
+  # === default_file_read
+  #
+  # This variant will use File.read().
+  # ========================================================================= #
+  def default_file_read(i)
+    File.read(i) if File.exist?(i)
+  end
+
+end; end

data/lib/bioroebe/base/colours_for_base/colours_for_base.rb

@@ -209,14 +209,6 @@ module ColoursForBase # === Bioroebe::ColoursForBase
     return i
   end
 
-  # ========================================================================= #
-  # === sfancy
-  # ========================================================================= #
-  def sfancy(i = '')
-    return powderblue(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
-    return i
-  end
-
   # ========================================================================= #
   # === simp
   # ========================================================================= #
@@ -272,4 +264,22 @@ module ColoursForBase # === Bioroebe::ColoursForBase
     @use_colours = true
   end
 
+  # ========================================================================= #
+  # === efancy
+  # ========================================================================= #
+  def efancy(i)
+    e sfancy(i)
+  end
+
+  # ========================================================================= #
+  # === sfancy
+  # ========================================================================= #
+  def sfancy(
+      i           = '',
+      use_colours = use_colours?
+    )
+    return powderblue(i) if use_colours and use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
 end; end

data/lib/bioroebe/base/commandline_application/commandline_application.rb

@@ -8,20 +8,21 @@
 require 'bioroebe/base/colours.rb'
 require 'bioroebe/base/prototype/prototype.rb'
 require 'bioroebe/base/misc.rb' # ← This file contains the is_palindrome? check.
-require 'bioroebe/base/commandline_application/aminoacids.rb'
-require 'bioroebe/base/commandline_application/commandline_arguments.rb'
-require 'bioroebe/base/commandline_application/directory.rb'
-require 'bioroebe/base/commandline_application/extract.rb'
-require 'bioroebe/base/commandline_application/misc.rb'
-require 'bioroebe/base/commandline_application/opn.rb'
-require 'bioroebe/base/commandline_application/reset.rb'
-require 'bioroebe/base/commandline_application/warnings.rb'
-require 'bioroebe/base/commandline_application/write_what_into.rb'
 
 module Bioroebe
 
 class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
 
+  require 'bioroebe/base/commandline_application/aminoacids.rb'
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  require 'bioroebe/base/commandline_application/directory.rb'
+  require 'bioroebe/base/commandline_application/extract.rb'
+  require 'bioroebe/base/commandline_application/misc.rb'
+  require 'bioroebe/base/commandline_application/opn.rb'
+  require 'bioroebe/base/commandline_application/reset.rb'
+  require 'bioroebe/base/commandline_application/warnings.rb'
+  require 'bioroebe/base/commandline_application/write_what_into.rb'
+
   require 'bioroebe/constants/nucleotides.rb'
   require 'bioroebe/constants/misc.rb'
   require 'bioroebe/constants/urls.rb'
@@ -34,4 +35,7 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
   include Bioroebe::ColoursForBase
   include Bioroebe::CommandlineArguments
 
+  require 'bioroebe/base/base_module/base_module.rb'
+  include Bioroebe::BaseModule
+
 end; end

data/lib/bioroebe/base/commandline_application/commandline_arguments.rb

@@ -68,17 +68,6 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     @commandline_arguments.reject {|entry| File.file?(entry.to_s) }
   end
 
-  # ========================================================================= #
-  # === return_entries_without_two_leading_hyphens
-  #
-  # This variant will return all entries WITHOUT leading hyphens.
-  # ========================================================================= #
-  def return_entries_without_two_leading_hyphens(
-      i = @commandline_arguments
-    )
-    i.reject {|entry| entry.start_with? '--' }
-  end; alias return_commandline_arguments_without_hyphen return_entries_without_two_leading_hyphens # === return_commandline_arguments_without_hyphen
-
   # ========================================================================= #
   # === select_commandline_arguments
   #
@@ -111,6 +100,13 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     @commandline_arguments.join(' ').strip
   end
 
+  # ========================================================================= #
+  # === first_non_hyphen_argument?
+  # ========================================================================= #
+  def first_non_hyphen_argument?
+    return_entries_without_two_leading_hyphens.first
+  end; alias first_non_hyphened_argument? first_non_hyphen_argument? # === first_non_hyphened_argument?
+
   # ========================================================================= #
   # === select_entries_starting_with_two_hyphens
   #
@@ -125,20 +121,29 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
     else
       []
     end
-  end; alias commandline_arguments_with_two_leading_hyphens         select_entries_starting_with_two_hyphens # === commandline_arguments_with_two_leading_hyphens
-       alias commandline_arguments_containing_hyphens?              select_entries_starting_with_two_hyphens # === commandline_arguments_containing_hyphens?
-       alias return_entries_with_two_leading_hyphens_from           select_entries_starting_with_two_hyphens # === return_entries_with_two_leading_hyphens_from
+  end; alias return_entries_with_two_leading_hyphens_from           select_entries_starting_with_two_hyphens # === return_entries_with_two_leading_hyphens_from
        alias return_arguments_with_leading_hyphens                  select_entries_starting_with_two_hyphens # === return_arguments_with_leading_hyphens
        alias return_commandline_arguments_starting_with_hyphens     select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_hyphens
        alias return_commandline_arguments_starting_with_two_hyphens select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_two_hyphens
-       alias select_two_hyphens_from                                select_entries_starting_with_two_hyphens # === select_two_hyphens_from
+       alias commandline_arguments_containing_hyphens?              select_entries_starting_with_two_hyphens # === commandline_arguments_containing_hyphens?
+       alias commandline_arguments_containing_leading_hyphens?      select_entries_starting_with_two_hyphens # === commandline_arguments_containing_leading_hyphens?
+       alias commandline_arguments_with_two_leading_hyphens         select_entries_starting_with_two_hyphens # === commandline_arguments_with_two_leading_hyphens
        alias commandline_arguments_starting_with_leading_hyphens?   select_entries_starting_with_two_hyphens # === commandline_arguments_starting_with_leading_hyphens?
+       alias commandline_arguments_starting_with_a_hyphen?          select_entries_starting_with_two_hyphens # === commandline_arguments_starting_with_a_hyphen?
+       alias commandline_arguments_starting_with_a_hyphen           select_entries_starting_with_two_hyphens # === commandline_arguments_starting_with_a_hyphen
+       alias select_two_hyphens_from                                select_entries_starting_with_two_hyphens # === select_two_hyphens_from
 
   # ========================================================================= #
-  # === first_non_hyphen_argument?
+  # === return_entries_without_two_leading_hyphens
+  #
+  # This variant will return all entries WITHOUT leading hyphens.
   # ========================================================================= #
-  def first_non_hyphen_argument?
-    return_entries_without_two_leading_hyphens.first
-  end; alias first_non_hyphened_argument? first_non_hyphen_argument? # === first_non_hyphened_argument?
+  def return_entries_without_two_leading_hyphens(
+      i = @commandline_arguments
+    )
+    i.reject {|entry| entry.start_with? '--' }
+  end; alias return_commandline_arguments_without_hyphen return_entries_without_two_leading_hyphens # === return_commandline_arguments_without_hyphen
+       alias reject_hyphens                              return_entries_without_two_leading_hyphens # === reject_hyphens
+       alias non_hyphened_commandline_arguments?         return_entries_without_two_leading_hyphens # === non_hyphened_commandline_arguments?
 
 end; end

data/lib/bioroebe/base/commandline_application/misc.rb

@@ -163,17 +163,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     ::Bioroebe.cat(i)
   end
 
-  # ========================================================================= #
-  # === codon_to_aminoacid
-  # ========================================================================= #
-  def codon_to_aminoacid(i)
-    unless Bioroebe.respond_to? :codon_to_aminoacid
-      require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
-    end
-    ::Bioroebe.codon_to_aminoacid(i)
-  end; alias nucleotides_to_aminoacid codon_to_aminoacid # === nucleotides_to_aminoacid
-       alias codons_to_aminoacid      codon_to_aminoacid # === codons_to_aminoacid
-
   # ========================================================================= #
   # === without_extname
   #
@@ -329,23 +318,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     ::Bioroebe.return_ubiquitin_sequence(i)
   end
 
-  # ========================================================================= #
-  # === be_verbose?
-  # ========================================================================= #
-  def be_verbose?
-    @be_verbose
-  end; alias verbose? be_verbose? # === be_verbose?
-
-  # ========================================================================= #
-  # === be_silent
-  # ========================================================================= #
-  def be_silent
-    @be_verbose = false
-  end; alias be_quiet          be_silent # === be_quiet
-       alias set_be_silent     be_silent # === set_be_silent
-       alias set_be_quiet      be_silent # === set_be_quiet
-       alias do_not_be_verbose be_silent # === do_not_be_verbose
-
   # ========================================================================= #
   # === leading_five_prime
   #
@@ -392,19 +364,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     )
   end
 
-  # ========================================================================= #
-  # === set_be_verbose
-  # ========================================================================= #
-  def set_be_verbose(i = true)
-    case i
-    when :be_verbose
-      i = true
-    when :be_quiet
-      i = false
-    end
-    @be_verbose = i
-  end
-
   # ========================================================================= #
   # === colourize_this_dna_sequence
   #
@@ -435,14 +394,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     return i.delete('[0-9]')
   end
 
-  require 'bioroebe/toplevel_methods/open_in_browser.rb'
-  # ========================================================================= #
-  # === open_in_browser
-  # ========================================================================= #
-  def open_in_browser(this_url)
-    ::Bioroebe.open_in_browser(this_url)
-  end
-
   # ========================================================================= #
   # === load_bioroebe_yaml_file
   #
@@ -482,4 +433,70 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
   end; alias three_aminoacid_letter_code_to_one_aminoacid_letter_code three_to_one # === three_aminoacid_letter_code_to_one_aminoacid_letter_code
        alias three_letters_to_one_letter                              three_to_one # === three_letters_to_one_letter
 
+  require 'bioroebe/toplevel_methods/open_in_browser.rb'
+  # ========================================================================= #
+  # === open_in_browser
+  # ========================================================================= #
+  def open_in_browser(this_url)
+    ::Bioroebe.open_in_browser(this_url)
+  end; alias open_in_browser_tab open_in_browser # === open_in_browser_tab
+
+  require 'bioroebe/toplevel_methods/verbose.rb'
+  # ========================================================================= #
+  # === verbose_truth
+  #
+  # Delegate towards the module Bioroebe::VerboseTruth here.
+  # ========================================================================= #
+  def verbose_truth(i)
+    ::Bioroebe::VerboseTruth[i]
+  end
+
+  # ========================================================================= #
+  # === codon_to_aminoacid
+  # ========================================================================= #
+  def codon_to_aminoacid(i)
+    unless Bioroebe.respond_to? :codon_to_aminoacid
+      require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
+    end
+    ::Bioroebe.codon_to_aminoacid(i).to_s
+  end; alias nucleotides_to_aminoacid codon_to_aminoacid # === nucleotides_to_aminoacid
+       alias codons_to_aminoacid      codon_to_aminoacid # === codons_to_aminoacid
+
+  # ========================================================================= #
+  # === be_verbose?
+  # ========================================================================= #
+  def be_verbose?
+    @internal_hash[:be_verbose]
+  end; alias verbose? be_verbose? # === be_verbose?
+
+  # ========================================================================= #
+  # === be_silent
+  # ========================================================================= #
+  def be_silent
+    @internal_hash[:be_verbose] = false
+  end; alias be_quiet          be_silent # === be_quiet
+       alias set_be_silent     be_silent # === set_be_silent
+       alias set_be_quiet      be_silent # === set_be_quiet
+       alias do_not_be_verbose be_silent # === do_not_be_verbose
+
+  # ========================================================================= #
+  # === set_be_verbose
+  # ========================================================================= #
+  def set_be_verbose(i = true)
+    case i
+    # ======================================================================= #
+    # === :be_verbose
+    # ======================================================================= #
+    when :be_verbose,
+         :default
+      i = true
+    # ======================================================================= #
+    # === :be_quiet
+    # ======================================================================= #
+    when :be_quiet
+      i = false
+    end
+    @internal_hash[:be_verbose] = i
+  end
+
 end; end

data/lib/bioroebe/base/commandline_application/opn.rb

@@ -22,18 +22,11 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     ::Bioroebe.use_opn?
   end
 
-  # ========================================================================= #
-  # === opne
-  # ========================================================================= #
-  def opne(i = '')
-    opnn; e i
-  end
-
   # ========================================================================= #
   # === opnn
   # ========================================================================= #
   def opnn(
-      i = @namespace,
+      i = namespace?,
       &block
     )
     if use_opn?
@@ -44,4 +37,11 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     end
   end
 
+  # ========================================================================= #
+  # === opne
+  # ========================================================================= #
+  def opne(i = '')
+    opnn; erev i
+  end
+
 end; end