bioroebe 0.10.80 → 0.11.25

data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb

@@ -49,68 +49,6 @@ module Bioroebe
     end
   end
 
-  # ========================================================================= #
-  # === Bioroebe.colourize_this_fasta_dna_sequence
-  #
-  # This toplevel method can be used to colourize a FASTA (DNA)
-  # sequence, e. g. "ATGCGCGTATTA" and so forth.
-  #
-  # Note that this is intended for the commandline, that is to be
-  # displayed on e. g. a KDE Konsole terminal.
-  #
-  # Usage example:
-  #
-  #   puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA')
-  #
-  # ========================================================================= #
-  def self.colourize_this_fasta_dna_sequence(
-      i = nil
-    )
-    if i.nil?
-      e 'Please provide a valid FASTA sequence as input to '\
-        'Bioroebe.colourize_this_fasta_dna_sequence()'
-      return
-    end
-    if i.is_a? Array
-      # ===================================================================== #
-      # Arrays will be joined together.
-      # ===================================================================== #
-      i = i.join(' ').strip
-    end
-    if i.is_a? String
-      # ===================================================================== #
-      # The colours are either defined in a file called
-      # 'colourize_fasta_sequences.yml' or they are simply hardcoded.
-      #
-      # The preferred (and thus default) way is to simply make use
-      # of that .yml file. That works on my home system, so it
-      # should work for other people as well.
-      # ===================================================================== #
-      if use_colours?
-        i = i.dup if i.frozen?
-        this_file = FILE_COLOURIZE_FASTA_SEQUENCES
-        if File.exist? this_file
-          dataset_for_the_colours = YAML.load_file(this_file)
-          dataset_for_the_colours.each_pair {|this_nucleotide, this_colour_to_be_used|
-            i.gsub!(
-              /#{this_nucleotide}/,
-              send(this_colour_to_be_used, this_nucleotide)+
-              rev
-            )
-          }
-        else
-          i.gsub!(/A/, "#{teal('A')}#{rev}")
-          i.gsub!(/C/, "#{slateblue('C')}#{rev}")
-          i.gsub!(/G/, "#{royalblue('G')}#{rev}")
-          i.gsub!(/T/, "#{steelblue('T')}#{rev}")
-          i.gsub!(/U/, "#{steelblue('U')}#{rev}") # Uracil is just the same as Thymine.
-        end
-      end
-    end
-    i
-  end; self.instance_eval { alias colourize_this_fasta_sequence colourize_this_fasta_dna_sequence } # === Bioroebe.colourize_this_fasta_sequence
-       self.instance_eval { alias colourized_parse_fasta        colourize_this_fasta_dna_sequence } # === Bioroebe.colourized_parse_fasta
-
   # ========================================================================= #
   # === Bioroebe.calculate_weight_of_the_aminoacids_in_this_fasta_file
   #
@@ -317,13 +255,113 @@ module Bioroebe
     end
   end
 
+  # ========================================================================= #
+  # === Bioroebe.colourize_this_fasta_dna_sequence
+  #
+  # This toplevel method can be used to colourize a FASTA (DNA)
+  # sequence, e. g. "ATGCGCGTATTA" and so forth.
+  #
+  # Note that this is intended for the commandline, that is to be
+  # displayed on e. g. a KDE Konsole terminal.
+  #
+  # Usage examples:
+  #
+  #   puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA')
+  #   puts Bioroebe.colourize_this_fasta_dna_sequence('ATGCGCATGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA') { :with_ruler }
+  #   puts Bioroebe.colourize_this_fasta_dna_sequence('TGCGCGTATTAGTATTAATGCGCGTATTAATGCGCGTATTA') { :with_ruler_steelblue_colour }
+  #
+  # ========================================================================= #
+  def self.colourize_this_fasta_dna_sequence(
+      i = nil,
+      &block
+    )
+    unless ::Bioroebe.respond_to?(:ruler_return_as_string_without_colours)
+      require 'bioroebe/misc/ruler.rb'
+    end
+    if i.nil?
+      e 'Please provide a valid FASTA sequence as input to '\
+        'Bioroebe.colourize_this_fasta_dna_sequence()'
+      return
+    end
+    if i.is_a? Array
+      # ===================================================================== #
+      # Arrays will be joined together.
+      # ===================================================================== #
+      i = i.join(' ').strip
+    end
+    original_input = i.dup
+    i = i.dup # Always dup it here.
+    if i.is_a? String
+      # ===================================================================== #
+      # The colours are either defined in a file called
+      # 'colourize_fasta_sequences.yml' or they are simply hardcoded.
+      #
+      # The preferred (and thus default) way is to simply make use
+      # of that .yml file. That works on my home system, so it
+      # should work for other people as well.
+      # ===================================================================== #
+      if use_colours?
+        this_file = FILE_COLOURIZE_FASTA_SEQUENCES
+        if File.exist? this_file
+          dataset_for_the_colours = YAML.load_file(this_file)
+          dataset_for_the_colours.each_pair {|this_nucleotide, this_colour_to_be_used|
+            i.gsub!(
+              /#{this_nucleotide}/,
+              send(this_colour_to_be_used, this_nucleotide)+
+              rev
+            )
+          }
+        else
+          i.gsub!(/A/, "#{teal('A')}#{rev}")
+          i.gsub!(/C/, "#{slateblue('C')}#{rev}")
+          i.gsub!(/G/, "#{royalblue('G')}#{rev}")
+          i.gsub!(/T/, "#{steelblue('T')}#{rev}")
+          i.gsub!(/U/, "#{steelblue('U')}#{rev}") # Uracil is just the same as Thymine.
+        end
+      end
+    end
+    # ======================================================================= #
+    # === Handle blocks next
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+      case yielded
+      # ===================================================================== #
+      # === with_ruler
+      # ===================================================================== #
+      when :with_ruler,
+           :add_ruler,
+           :ruler
+        i.prepend(
+          ::Bioroebe.ruler_return_as_string_without_colours(original_input)+
+          "\n"
+        )
+      else # Assume something like:
+           #   :with_ruler_steelblue_colour
+        if yielded.to_s.include? 'colo' # This assumes "colour" or "color".
+          use_this_colour = yielded.to_s.sub(/_colou?r/,'').
+                                         sub(/with_ruler_/,'')
+          this_string = send(use_this_colour,
+            ::Bioroebe.ruler_return_as_string_without_colours(original_input)+
+            "\n"
+          )
+          i.prepend(this_string)
+        end
+      end
+    end
+    return i
+  end; self.instance_eval { alias colourize_this_fasta_sequence colourize_this_fasta_dna_sequence } # === Bioroebe.colourize_this_fasta_sequence
+       self.instance_eval { alias colourized_parse_fasta        colourize_this_fasta_dna_sequence } # === Bioroebe.colourized_parse_fasta
+
   # ========================================================================= #
   # === Bioroebe.show_fasta_header
   #
   # This ad-hoc method can be used to quickly show the first line of an
   # assumed .fasta file.
   # ========================================================================= #
-  def self.show_fasta_header(of_this_file)
+  def self.show_fasta_header(
+      of_this_file
+    )
     if of_this_file.is_a? Array
       of_this_file = of_this_file.first
     end

data/lib/bioroebe/toplevel_methods/misc.rb

@@ -15,22 +15,6 @@ module Bioroebe
   require 'bioroebe/toplevel_methods/esystem.rb'
   require 'bioroebe/toplevel_methods/extract.rb'
 
-  # ========================================================================= #
-  # === Bioroebe.thousand_percentage
-  #
-  # This method is solely a helper-method for Bioroebe.frequency_per_thousand().
-  # ========================================================================= #
-  def self.thousand_percentage(
-      this_codon_n_times =   1,
-      total_n_elements  = 1000
-    )
-    result = (
-      (this_codon_n_times * 1000.0) / total_n_elements.to_f
-    ).round(1)
-    padded_result = result.to_s.rjust(5, ' ')
-    return padded_result
-  end
-
   # ========================================================================= #
   # === Bioroebe.frequency_per_thousand
   #
@@ -86,6 +70,7 @@ EOF
   # Usage example:
   #
   #   Bioroebe.codon_frequency_of_this_string
+  #   Bioroebe.codon_frequency_of_this_string 'ATTCGTACGATCGACTACTACT' # => {"UAC"=>2, "GAC"=>1, "AUC"=>1, "ACG"=>1, "CGU"=>1, "AUU"=>1}
   #
   # ========================================================================= #
   def self.codon_frequency_of_this_string(
@@ -107,6 +92,22 @@ EOF
     return sorted_hash
   end
 
+  # ========================================================================= #
+  # === Bioroebe.thousand_percentage
+  #
+  # This method is solely a helper-method for Bioroebe.frequency_per_thousand().
+  # ========================================================================= #
+  def self.thousand_percentage(
+      this_codon_n_times =   1,
+      total_n_elements  = 1000
+    )
+    result = (
+      (this_codon_n_times * 1000.0) / total_n_elements.to_f
+    ).round(1)
+    padded_result = result.to_s.rjust(5, ' ')
+    return padded_result
+  end
+
   # ========================================================================= #
   # === Bioroebe.align_this_string_via_multiple_sequence_alignment
   #

data/lib/bioroebe/toplevel_methods/nucleotides.rb

@@ -270,12 +270,19 @@ module Bioroebe
   #   Bioroebe.random_dna 15 # => "TTGGTAAGCTCTTTA"
   #   Bioroebe.random_dna 25 # => "TTAGCACAAGCATGGACGGACCAGA"
   #   Bioroebe.random_dna(50, { A: 10, T: 10, C: 10, G: 70}) # => "GGGGTGGGGAGGGTATGCGGAGGAAGGGCGGGAAGGGCGGGGGCTGGGCG"
+  #   Bioroebe.random_dna(20, 'ATGGGGGGGG') # => "TGAGGGGGGGGGTGGGAGGG"
+  #   Bioroebe.random_dna(20, 'ATGGGGGGGG') # => "GGTAGGGGGGGGTAGGGGGG"
   #
   # ========================================================================= #
   def self.generate_random_dna_sequence(
-      i = ARGV,
-      optional_hash_with_the_frequencies = {}
+      i                                  = ARGV,
+      optional_hash_with_the_frequencies = {} # ← This may be a String too, mind you.
     )
+    # ======================================================================= #
+    # First define our result-String. This one will be returned by this
+    # method.
+    # ======================================================================= #
+    result = ''.dup
     _ = Bioroebe::DNA_NUCLEOTIDES # Get a handle to the four DNA nucleotides.
     if i.is_a? Array
       i = i.join.strip
@@ -284,9 +291,19 @@ module Bioroebe
     when :default
       i = 250
     end
-    i = i.to_i
-    result = ''.dup
-    if optional_hash_with_the_frequencies.empty?
+    i = i.to_i # This is "n times".
+    # ======================================================================= #
+    # First handle the case where the user passed a String:
+    # ======================================================================= #
+    if optional_hash_with_the_frequencies.is_a? String
+      pool = optional_hash_with_the_frequencies.dup.chars.shuffle
+      i.times {
+        if pool.size == 0
+          pool = optional_hash_with_the_frequencies.dup.chars.shuffle
+        end
+        result << pool.pop
+      }
+    elsif optional_hash_with_the_frequencies.empty?
       # ===================================================================== #
       # This is the default clause.
       # ===================================================================== #

data/lib/bioroebe/toplevel_methods/open_in_browser.rb

@@ -18,6 +18,8 @@ module Bioroebe
   # This constant specifies the default browser to use for the
   # bioroebe-project.
   # ========================================================================= #
+  # /home/x/programming/ruby/src/bioroebe/lib/bioroebe/yaml/configuration/browser.yml
+  # ========================================================================= #
   if File.exist? "#{project_yaml_directory?}browser.yml"
     USE_THIS_BROWSER = YAML.load_file(FILE_BROWSER)
   elsif ENV['BROWSER']

data/lib/bioroebe/toplevel_methods/palindromes.rb

@@ -115,8 +115,7 @@ module Bioroebe
 end
 
 if __FILE__ == $PROGRAM_NAME
-pp Bioroebe.every_reverse_palindrome_in_this_string(ARGV)
-exit
+  pp Bioroebe.every_reverse_palindrome_in_this_string(ARGV)
   if ARGV.empty?
     p 'GAATTC: '+Bioroebe.is_palindrome?('GAATTC').to_s   # => true
     p 'GAATTCCC: '+Bioroebe.is_palindrome?('GAATTCCC').to_s # => false

data/lib/bioroebe/toplevel_methods/taxonomy.rb

@@ -141,8 +141,8 @@ module Taxonomy # === Bioroebe::Taxonomy
       end
     end
     if be_verbose
-      e 'Now trying to change to the base directory at '+
-        ::Bioroebe.sdir(this_dir)+'.'
+      e "Now trying to change to the base directory at "\
+        "#{::Bioroebe.sdir(this_dir)}."
     end
     cd this_dir
     e N+'We will next attempt to download the file `'+

data/lib/bioroebe/toplevel_methods/to_camelcase.rb

@@ -11,6 +11,11 @@ module Bioroebe
   # === Bioroebe.to_camelcase
   #
   # Convert the given String (the input) into a camelcased variant.
+  #
+  # Usage example:
+  #
+  #   Bioroebe.to_camelcase('foo_bar') # => "FooBar"
+  #
   # ========================================================================= #
   def self.to_camelcase(i)
     if i.is_a? Array

data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb

@@ -35,11 +35,6 @@ class AlignOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe
   require 'bioroebe/regexes/regexes.rb'
   require 'bioroebe/codons/codons.rb'
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === START_CODON
   # ========================================================================= #
@@ -67,10 +62,7 @@ class AlignOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb

@@ -19,11 +19,6 @@ module Bioroebe
 
 class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::CheckForMismatches
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === COLOUR_TO_BE_USED_FOR_A_MISMATCH
   #
@@ -49,10 +44,7 @@ class CheckForMismatches < ::Bioroebe::CommandlineApplication # === Bioroebe::Ch
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace         = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @first_sequence
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/compacter.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class Compacter < ::Bioroebe::CommandlineApplication # === Bioroebe::Compacter
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -52,10 +47,7 @@ class Compacter < ::Bioroebe::CommandlineApplication # === Bioroebe::Compacter
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @ask_for_user_input
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/compseq/compseq.rb

@@ -47,11 +47,6 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
   # ========================================================================= #
   COLOURIZE_CpG_ISLANDS = true
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === EXPECTED_FREQUENCY
   # ========================================================================= #
@@ -108,10 +103,7 @@ class Compseq < ::Bioroebe::CommandlineApplication # === Bioroebe::Compseq
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @identifier
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb

@@ -44,11 +44,6 @@ https://www.ncbi.nlm.nih.gov/nuccore/NZ_CP007215.2
 https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2
 '
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -66,10 +61,7 @@ https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
   end
 
   # ========================================================================= #

data/lib/bioroebe/utility_scripts/dot_alignment.rb

@@ -21,11 +21,6 @@ module Bioroebe
 
 class DotAlignment < ::Bioroebe::CommandlineApplication # === Bioroebe::DotAlignment
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -43,10 +38,7 @@ class DotAlignment < ::Bioroebe::CommandlineApplication # === Bioroebe::DotAlign
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @may_we_continue
     # ======================================================================= #

data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb

@@ -42,10 +42,7 @@ class MoveFileToItsCorrectLocation < ::Bioroebe::CommandlineApplication
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @try_to_relocate_the_file_to_an_appropriate_subdirectory
     #

data/lib/bioroebe/utility_scripts/showorf/constants.rb

@@ -6,11 +6,6 @@ module Bioroebe
 
 class ShowOrf < ::Bioroebe::CommandlineApplication
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === COLOURIZE_VERTICAL_TOKEN
   # ========================================================================= #

data/lib/bioroebe/utility_scripts/showorf/reset.rb

@@ -11,10 +11,7 @@ class ShowOrf < ::Bioroebe::CommandlineApplication
   # ========================================================================= #
   def reset
     super()
-    # ======================================================================= #
-    # === @namespace
-    # ======================================================================= #
-    @namespace = NAMESPACE
+    infer_the_namespace
     # ======================================================================= #
     # === @show_these_frames
     #

data/lib/bioroebe/version/version.rb

@@ -9,7 +9,7 @@ module Bioroebe
   # ========================================================================= #
   # === VERSION
   # ========================================================================= #
-  VERSION = '0.10.80'
+  VERSION = '0.11.25'
 
   # ========================================================================= #
   # === LAST_UPDATE
@@ -17,7 +17,7 @@ module Bioroebe
   # This variable keeps track as to when the bioroebe project was last
   # updated. The notation is: DD.MM.YYYY
   # ========================================================================= #
-  LAST_UPDATE = '24.06.2022'
+  LAST_UPDATE = '18.08.2022'
 
   # ========================================================================= #
   # === URL_TO_THE_DOCUMENTATION