bioroebe 0.10.80 → 0.12.24

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

@@ -17,20 +17,22 @@ module CommandlineArguments # === Bioroebe::CommandlineApplication
   # ========================================================================= #
   def reset
     super()
+    reset_the_internal_hash
     # ======================================================================= #
     # === @namespace
     # ======================================================================= #
-    @namespace = Bioroebe::Base::NAMESPACE
+    # @namespace = Bioroebe::Base::NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @commandline_arguments
     # ======================================================================= #
     @commandline_arguments = []
     # ======================================================================= #
-    # === @be_verbose
+    # === :be_verbose
     #
     # By default, CommandlineApplication will report a lot of stuff.
     # ======================================================================= #
-    @be_verbose  = true
+    set_be_verbose
     # ======================================================================= #
     # === @use_colours
     # ======================================================================= #

data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb

@@ -0,0 +1,42 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::InternalHashModule
+#
+# Usage example:
+#
+#   Bioroebe::InternalHashModule.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/base/internal_hash_module/internal_hash_module.rb'
+# include Bioroebe::InternalHashModule
+# =========================================================================== #
+module Bioroebe
+
+module InternalHashModule # === Bioroebe::InternalHashModule
+
+  # ========================================================================= #
+  # === reset_the_internal_hash
+  # ========================================================================= #
+  def reset_the_internal_hash
+    # ======================================================================= #
+    # === @internal_hash
+    # ======================================================================= #
+    @internal_hash = {}
+  end
+
+  # ========================================================================= #
+  # === internal_hash?
+  #
+  # Query-method over the @internal_hash instance variable.
+  # ========================================================================= #
+  def internal_hash?
+    @internal_hash
+  end; alias ihash? internal_hash? # === ihash?
+
+end; end
+
+if __FILE__ == $PROGRAM_NAME
+  include Bioroebe::InternalHashModule
+end # internal_hash_module.rb

data/lib/bioroebe/base/misc.rb

@@ -10,6 +10,13 @@ class Base
 
   require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
 
+  # ========================================================================= #
+  # === namespace?
+  # ========================================================================= #
+  def namespace?
+    @namespace
+  end
+
   # ========================================================================= #
   # === is_palindrome?
   # ========================================================================= #
@@ -91,4 +98,32 @@ class Base
     ::Bioroebe.project_yaml_directory?
   end; alias yaml_directory? project_yaml_directory? # === yaml_directory?
 
+  # ========================================================================= #
+  # === infer_the_namespace
+  #
+  # This will assume the true namespace from the inspectable name.
+  # ========================================================================= #
+  def infer_the_namespace
+    _ = inspect.to_s.delete('<')
+    _ = _.split(':0').first if _.include?(':0')
+    if _.include? ' '
+      _ = _.split(' ').first.delete('#')
+      if _.include? ':'
+        _ = _.split(':')[0 .. -2].reject {|entry| entry.empty? }.join('::')
+      end
+    end
+    _.delete!('#') if _.include?('#')
+    @namespace = _ # And assign it here.
+  end
+
+  # ========================================================================= #
+  # === word_wrap
+  # ========================================================================= #
+  def word_wrap(
+      text,
+      line_width = 80
+    )
+    return text.scan(/\S.{0,#{line_width}}\S(?=\s|$)|\S+/).join(N)
+  end
+
 end; end

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

@@ -6,19 +6,32 @@
 # =========================================================================== #
 module Bioroebe
 
-class Base
+class Base # === Bioroebe::Base
 
   require 'bioroebe/requires/require_encoding.rb'
   require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
   require 'bioroebe/toplevel_methods/rds.rb'
 
+  require 'bioroebe/base/base_module/base_module.rb'
+  include Bioroebe::BaseModule
+
+  # ========================================================================= #
+  # === return_the_first_line_of_this_file
+  # ========================================================================= #
+  def return_the_first_line_of_this_file(i)
+    if File.exist? i
+      return File.open(i) {|this_file| this_file.readline.strip }
+    end
+    return i
+  end
+
   require 'bioroebe/toplevel_methods/is_on_roebe.rb'
   # ========================================================================= #
   # === is_on_roebe?
   # ========================================================================= #
   def is_on_roebe?
     ::Bioroebe.is_on_roebe?
-  end
+  end; alias on_roebe? is_on_roebe? # === on_roebe?
 
   # ========================================================================= #
   # === main_encoding?
@@ -98,11 +111,4 @@ class Base
     ::Bioroebe.no_file_exists_at(i)
   end
 
-  # ========================================================================= #
-  # === file_readlines
-  # ========================================================================= #
-  def file_readlines(i)
-    File.readlines(i, encoding: main_encoding?)
-  end; alias readlines file_readlines # === readlines
-
 end; end

data/lib/bioroebe/base/prototype/reset.rb

@@ -13,6 +13,9 @@ module Bioroebe
 
 class Base
 
+  require 'bioroebe/base/internal_hash_module/internal_hash_module.rb'
+  include Bioroebe::InternalHashModule
+
   # ========================================================================= #
   # === reset                                                     (reset tag)
   # ========================================================================= #
@@ -23,4 +26,11 @@ class Base
     @namespace = NAMESPACE # We store the namespace here.
   end
 
+  # # ========================================================================= #
+  # # === reset_the_internal_hash
+  # # ========================================================================= #
+  # def reset_the_internal_hash
+  #   @internal_hash = {}
+  # end
+
 end; end

data/lib/bioroebe/cleave_and_digest/digestion.rb

@@ -25,10 +25,18 @@ class Digestion < ::Bioroebe::CommandlineApplication # === Bioroebe::Digestion
   # ========================================================================= #
   def reset
     super()
+    reset_the_internal_hash # Always allow for @internal_hash to exist here.
     # ======================================================================= #
-    # === @show_the_weight_of_these_aminoacids
+    # === :show_the_weight_of_these_aminoacids
     # ======================================================================= #
-    @show_the_weight_of_these_aminoacids = true
+    @internal_hash[:show_the_weight_of_these_aminoacids] = true
+  end
+
+  # ========================================================================= #
+  # === show_the_weight_of_these_aminoacids?
+  # ========================================================================= #
+  def show_the_weight_of_these_aminoacids?
+    @internal_hash[:show_the_weight_of_these_aminoacids]
   end
 
   # ========================================================================= #

data/lib/bioroebe/cleave_and_digest/trypsin.rb

@@ -4,7 +4,12 @@
 # =========================================================================== #
 # === Bioroebe::Trypsin
 #
-# This class will simulate a digestion done via Trypsine.
+# This class will simulate a digestion done via Trypsin. It is a
+# subclass of class Digestion.
+#
+# Trypsin is a serine protease. It will actually cleave proteins
+# into peptides with an average size of 700-1500 daltons. This makes
+# it ideally suited for application in Mass Spectrometry. 
 #
 # Usage example:
 #
@@ -27,12 +32,26 @@ class Trypsin < ::Bioroebe::Digestion # === Bioroebe::Trypsin
   # ========================================================================= #
   def initialize(
       commandline_arguments = nil,
-      run_already           = true
+      run_already           = true,
+      &block
     )
     reset
     set_commandline_arguments(
       commandline_arguments
     )
+    # ======================================================================= #
+    # === Handle blocks given to this method next
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+      case yielded
+      # ===================================================================== #
+      # === :be_quiet
+      # ===================================================================== #
+      when :be_quiet
+        set_be_quiet
+      end
+    end
     run if run_already
   end
 
@@ -41,17 +60,21 @@ class Trypsin < ::Bioroebe::Digestion # === Bioroebe::Trypsin
   # ========================================================================= #
   def reset
     super()
+    set_be_verbose
     # ======================================================================= #
     # === @array_cut_at_these_aminoacids
+    #
+    # This variable ensures that trypsine cuts after lysines (K) and
+    # arginines (R).
     # ======================================================================= #
     @array_cut_at_these_aminoacids = %w( K R )
     # ======================================================================= #
-    # === @array_peptide_fragments
+    # === :array_peptide_fragments
     #
     # This class will store the peptide fragments into this unsorted
     # Array.
     # ======================================================================= #
-    @array_peptide_fragments = []
+    @internal_hash[:array_peptide_fragments] = []
   end
 
   # ========================================================================= #
@@ -60,7 +83,8 @@ class Trypsin < ::Bioroebe::Digestion # === Bioroebe::Trypsin
   # This method will perform the digestion.
   # ========================================================================= #
   def perform_the_digestion(
-      array_cut_at_these_aminoacids = @array_cut_at_these_aminoacids
+      array_cut_at_these_aminoacids = 
+        @array_cut_at_these_aminoacids
     )
     # ======================================================================= #
     # Trypsin splits at K and R, so we split on that.
@@ -89,63 +113,78 @@ class Trypsin < ::Bioroebe::Digestion # === Bioroebe::Trypsin
   end
 
   # ========================================================================= #
-  # === report
+  # === display_the_result_similar_to_pp_output
+  # ========================================================================= #
+  def display_the_result_similar_to_pp_output
+    print '['
+    @result.each_with_index {|entry, index|
+      print entry
+      print ', ' unless index == (@result.size - 1)
+    }
+    print ']'
+    e
+  end
+
+  # ========================================================================= #
+  # === report                                                   (report tag)
   # ========================================================================= #
   def report
-    @array_peptide_fragments.clear
+    @internal_hash[:array_peptide_fragments].clear
     if @result.empty?
       erev 'No cut-sequence was found for Trypsin. (Make sure to '\
            'input an aminoacid sequence.)'
     else
       the_sequence = first?
-      print '['; @result.each_with_index {|entry, index|
-        print entry
-        print ', ' unless index == (@result.size - 1)
-      }; print ']'; e
-      erev 'The following peptide fragments would be obtained '\
-           'if this were to be cut via Trypsin:'
-      e
       old_position = 0
-      erev ''.ljust(36)+the_sequence
-      e ''.ljust(36)+
-        colourize_this_aminoacid_sequence_for_the_commandline(
-          the_sequence
-        )
-      e ''.ljust(36)+
-        mediumturquoise_1_to_10+
-        mediumturquoise_1_to_10+
-        mediumturquoise_1_to_10+
-        mediumturquoise_1_to_10+
-        mediumturquoise_1_to_10
-
+      if be_verbose?
+        display_the_result_similar_to_pp_output
+        erev 'The following peptide fragments would be obtained '\
+             'if this were to be cut via Trypsin:'
+        e
+        erev ''.ljust(36)+the_sequence
+        e ''.ljust(36)+
+          colourize_this_aminoacid_sequence_for_the_commandline(
+            the_sequence
+          )
+        e ''.ljust(36)+
+          mediumturquoise_1_to_10+
+          mediumturquoise_1_to_10+
+          mediumturquoise_1_to_10+
+          mediumturquoise_1_to_10+
+          mediumturquoise_1_to_10
+      end
       @result.each {|this_position|
         this_subsequence = the_sequence[old_position .. (this_position - 1)]
         old_position = this_position
-        erev '  after the aminoacid-position '+
-             sfancy(this_position.to_s.rjust(3))+
-             rev+
-             ': '+
-             steelblue(
-               this_subsequence
-             )+crimson('↓')+
-             rev
+        if be_verbose?
+          erev '  after the aminoacid-position '+
+               sfancy(this_position.to_s.rjust(3))+
+               rev+
+               ': '+
+               steelblue(
+                 this_subsequence
+               )+crimson('↓')+
+               rev
+        end
         # =================================================================== #
         # === Show the weight of these aminoacids, if instructed to do so
         # =================================================================== #
-        if @show_the_weight_of_these_aminoacids
-          weight_of_this_peptide_fragment = Bioroebe.weight_of_this_aminoacid?(
-            this_subsequence.split(//)
-          ).round(5)
-          @array_peptide_fragments << [
-            this_subsequence, weight_of_this_peptide_fragment
-          ]
+        weight_of_this_peptide_fragment = Bioroebe.weight_of_this_aminoacid?(
+          this_subsequence.split(//)
+        ).round(5)
+        @internal_hash[:array_peptide_fragments] << [
+          this_subsequence, weight_of_this_peptide_fragment
+        ]
+        if show_the_weight_of_these_aminoacids? and be_verbose?
           erev ''.ljust(36)+'Weight of this peptide fragment: '+
                olivedrab(weight_of_this_peptide_fragment.to_s)
-        end  
+        end
       }
-      e
-      unless @array_peptide_fragments.empty?
-        show_sorted_peptide_fragments(@array_peptide_fragments)
+      if be_verbose?
+        e
+        unless @internal_hash[:array_peptide_fragments].empty?
+          show_sorted_peptide_fragments(@internal_hash[:array_peptide_fragments])
+        end
       end
     end
   end
@@ -154,10 +193,11 @@ class Trypsin < ::Bioroebe::Digestion # === Bioroebe::Trypsin
   # === show_sorted_peptide_fragments
   # ========================================================================= #
   def show_sorted_peptide_fragments(
-      i = @array_peptide_fragments
+      i = @internal_hash[:array_peptide_fragments]
     )
     sorted = i.sort_by {|fragment, weight| weight}.reverse
-    erev 'Next, the five heaviest fragments will be shown:'
+    erev 'Next, the '+steelblue('five heaviest fragments')+
+         rev+' will be shown:'
     e
     # ======================================================================= #
     # Only the top 5 heaviest fragments will be shown:
@@ -181,12 +221,26 @@ class Trypsin < ::Bioroebe::Digestion # === Bioroebe::Trypsin
   # ========================================================================= #
   # === Bioroebe::Trypsin[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i)
   end
 
-end; end
+end
+
+# =========================================================================== #
+# === Bioroebe.return_array_from_tryptic_digest
+# =========================================================================== #
+def self.return_array_from_tryptic_digest(
+    of_this_sequence = ARGV
+  )
+  if of_this_sequence.is_a? Array
+    of_this_sequence = of_this_sequence.first
+  end
+  Bioroebe::Trypsin.new(of_this_sequence) { :be_quiet }
+end
+
+end
 
 if __FILE__ == $PROGRAM_NAME
   Bioroebe::Trypsin.new(ARGV)
-end # trypsin
+end # trypsin GGGRRRLSMLLLSLELERRLKKLKLRR

data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb

@@ -26,11 +26,6 @@ class ParseFrequencyTable < ::Bioroebe::CommandlineApplication # === Bioroebe::P
 
   require 'open-uri'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === AUTOMATICALLY_CREATE_A_LOCAL_YAML_FILE_IF_IT_DOES_NOT_YET_EXIST
   #
@@ -100,10 +95,7 @@ GUG 30.5(  4267)  GCG  8.6(  1207)  GAG 35.8(  5005)  GGG 15.6(  2181)'
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @use_this_url
     #
@@ -129,7 +121,7 @@ GUG 30.5(  4267)  GCG  8.6(  1207)  GAG 35.8(  5005)  GGG 15.6(  2181)'
   # === menu                                                       (menu tag)
   # ========================================================================= #
   def menu(
-      i = @commandline_arguments
+      i = commandline_arguments?
     )
     if i.is_a? Array
       i.each {|entry| menu(entry) }

data/lib/bioroebe/codons/codons.rb

@@ -24,7 +24,7 @@ module Bioroebe
   require 'bioroebe/constants/codon_tables.rb'
   require 'bioroebe/regexes/regexes.rb'
   require 'bioroebe/codons/codon_table.rb'
-  require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
+  # require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
 
   # ========================================================================= #
   # === @stop_codons