bioroebe 0.10.80 → 0.12.12

data/lib/bioroebe/toplevel_methods/nucleotides.rb

@@ -19,6 +19,102 @@ module Bioroebe
   require 'bioroebe/constants/nucleotides.rb'
   require 'bioroebe/toplevel_methods/e.rb'
 
+  # ========================================================================= #
+  # === Bioroebe.can_base_pair_with?
+  #
+  # Usage example:
+  #
+  #   Bioroebe.can_base_pair_with?('A','T') # => true
+  #   Bioroebe.can_base_pair_with?('A','G') # => false
+  #
+  # ========================================================================= #
+  def self.can_base_pair_with?(a, b)
+    ::Bioroebe.partner_nucleotide(a) == b
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.partner_nucleotide
+  #
+  # This small "table" will simply return the corresponding Nucleotide
+  # matching the given input at hand - in other words, the corresponding
+  # DNA nucleotide that can base-pair with the input nucleotide.
+  #
+  # Since this is a method call this may be a bit slow if you have to
+  # invoke the method repeatedly. In this case, you should consider
+  # using the method befined below, through the method
+  # Bioroebe.partner_nucleotide_hash(), and then use that Hash instead.
+  #
+  # Usage example:
+  #
+  #   Bioroebe.partner_nucleotide('A') # => "T"
+  #   Bioroebe.should_match_to?('T') # => "A"
+  #
+  # ========================================================================= #
+  def self.partner_nucleotide(i)
+    i = i.first if i.is_a? Array # We only handle the first entry in an Array.
+    if i
+      i = i.dup if i.frozen?
+      i.upcase! # just in caase.
+      case i # case tag.
+      when 'A'
+        return 'T'
+      when 'T','U'
+        return 'A'
+      when 'G'
+        return 'C'
+      when 'C'
+        return 'G'
+      else
+        return nil # means illegal value.
+      end
+    end
+    return i # Return just in case.
+  end; self.instance_eval { alias complementary_nucleotide partner_nucleotide } # === Bioroebe.complementary_nucleotide
+       self.instance_eval { alias return_dna_match         partner_nucleotide } # === Bioroebe.return_dna_match
+       self.instance_eval { alias should_match_to?         partner_nucleotide } # === Bioroebe.should_match_to?
+
+  # ========================================================================= #
+  # === Bioroebe.contains_an_inverted_repeat?
+  #
+  # We assume an inverted repeat to exist if at the least 2 nucleotides
+  # match to one another in the reverse, so a total of 4 matching
+  # nucleotides. This assumption may not necessarily be correct and
+  # we may have to fine-tune this at a later time.
+  #
+  # For testing purpose, the sequence 'TTACGAAAAAACGTAA' can be used. 
+  # ========================================================================= #
+  def self.contains_an_inverted_repeat?(
+      #i = 'AGCCCCGCAAAAAAGGCGGGCU'
+      i = 'TTACGAAAAAACGTAA' # This is in the 5'→3' direction.
+    )
+    contains_an_inverted_repeat = false
+    longest_stretch = 0
+    current_stretch = 0
+    halfed_position = i.size / 2
+    both_sides = [
+      i[0 .. (halfed_position-1)],
+      i[halfed_position .. -1]
+    ]
+    # ======================================================================= #
+    # Now that we have both sides, we will try to match them. First reverse
+    # the second, though.
+    # ======================================================================= #
+    first  = both_sides[0]
+    second = both_sides[1].reverse # Work via the reverse sequence.
+    first.chars.each_with_index {|this_nucleotide, index|
+      if can_base_pair_with?(second[index], this_nucleotide)
+        current_stretch += 1
+        longest_stretch = current_stretch if current_stretch > longest_stretch 
+      else
+        current_stretch = 0
+      end
+    }
+    if longest_stretch >= 2
+      contains_an_inverted_repeat = true
+    end
+    return contains_an_inverted_repeat
+  end
+
   # ========================================================================= #
   # === Bioroebe.complementary_rna_strand
   #
@@ -147,47 +243,6 @@ module Bioroebe
     return _.flatten.uniq.sort
   end
 
-  # ========================================================================= #
-  # === Bioroebe.partner_nucleotide
-  #
-  # This small "table" will simply return the corresponding Nucleotide
-  # matching the given input at hand - in other words, the corresponding
-  # DNA nucleotide that can base-pair with the input nucleotide.
-  #
-  # Since this is a method call this may be a bit slow if you have to
-  # invoke the method repeatedly. In this case, you should consider
-  # using the method befined below, through the method
-  # Bioroebe.partner_nucleotide_hash(), and then use that Hash instead.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.partner_nucleotide('A') # => "T"
-  #   Bioroebe.should_match_to?('T') # => "A"
-  #
-  # ========================================================================= #
-  def self.partner_nucleotide(i)
-    i = i.first if i.is_a? Array # We only handle the first entry in an Array.
-    if i
-      i = i.dup if i.frozen?
-      i.upcase! # just in caase.
-      case i # case tag.
-      when 'A'
-        return 'T'
-      when 'T','U'
-        return 'A'
-      when 'G'
-        return 'C'
-      when 'C'
-        return 'G'
-      else
-        return nil # means illegal value.
-      end
-    end
-    return i # Return just in case.
-  end; self.instance_eval { alias complementary_nucleotide partner_nucleotide } # === Bioroebe.complementary_nucleotide
-       self.instance_eval { alias return_dna_match         partner_nucleotide } # === Bioroebe.return_dna_match
-       self.instance_eval { alias should_match_to?         partner_nucleotide } # === Bioroebe.should_match_to?
-
   # ========================================================================= #
   # === Bioroebe.return_all_positions_of_this_nucleotide
   #
@@ -270,12 +325,19 @@ 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 +346,19 @@ 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/consensus_sequence.rb

@@ -35,7 +35,7 @@ class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::Con
       # ===================================================================== #
       when :do_not_run_yet_and_be_quiet
         run_already = false
-        @be_verbose = false
+        set_be_quiet
         @report_the_frequencies = false
       # ===================================================================== #
       # === :do_not_run_yet
@@ -46,7 +46,7 @@ class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::Con
       # === :be_quiet
       # ===================================================================== #
       when :be_quiet
-        @be_verbose = false
+        set_be_quiet
         @report_the_frequencies = false
       end
     end
@@ -66,7 +66,7 @@ class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::Con
     # ======================================================================= #
     # === @be_verbose
     # ======================================================================= #
-    @be_verbose = true
+    set_be_verbose
     # ======================================================================= #
     # === @report_the_frequencies
     # ======================================================================= #
@@ -195,7 +195,7 @@ class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::Con
   # === report_on_which_sequences_we_will_operate
   # ========================================================================= #
   def report_on_which_sequences_we_will_operate(
-      be_verbose = @be_verbose
+      be_verbose = be_verbose?
     )
     case be_verbose
     when :be_verbose
@@ -217,7 +217,7 @@ class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::Con
   # === report_the_consensus_sequence
   # ========================================================================= #
   def report_the_consensus_sequence
-    if @be_verbose
+    if be_verbose?
       the_consensus_sequence = consensus_sequence?
       erev 'The consensus sequence is: '
       e
@@ -238,7 +238,7 @@ class ConsensusSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::Con
         try_to_find_and_report_an_even_simpler_consensus_sequence(
           the_consensus_sequence
         )
-        if @be_verbose
+        if be_verbose?
           erev 'Finally, we will display the above findings in a'
           erev 'shorter variant:'
           report_on_which_sequences_we_will_operate

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/parse_taxonomy.rb

@@ -64,7 +64,7 @@ class ParseTaxonomy < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseTa
     # ======================================================================= #
     # === @be_verbose
     # ======================================================================= #
-    @be_verbose = false
+    set_be_quiet
   end
 
   # ========================================================================= #
@@ -112,7 +112,7 @@ class ParseTaxonomy < ::Bioroebe::CommandlineApplication # === Bioroebe::ParseTa
   # ========================================================================= #
   def read_in_url(i = @url)
     require 'open-uri'
-    e "Reading in from #{sfancy(i.to_s)} now." if @be_verbose
+    e "Reading in from #{sfancy(i.to_s)} now." if be_verbose?
     @dataset = URI.open(i).read
   end
 

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 = '0.12.12'
 
   # ========================================================================= #
   # === 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 = '28.01.2023'
 
   # ========================================================================= #
   # === URL_TO_THE_DOCUMENTATION