bioroebe 0.13.31 → 0.13.32

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 43cec66a457f6dfbccd9190fd8c692749601e5851940bfa102f898fef54851bc
-  data.tar.gz: 403c84a578f8502522ee67d8238faf56bd0e68a6f795708ebbe08428c4aac441
+  metadata.gz: e4355114ebcb4402b53e97959a6c5a244b4758af7f7f0fbac28e8fd52a3d3865
+  data.tar.gz: 3f5f816dae19cdf3134280dc780eb47702331c7264ef791010b3eadd934cf19e
 SHA512:
-  metadata.gz: 37e1fc899fc423b95b1a47a679f9a36de7526e50b7df5040edb67d39e79ef078ffab0f33f8ab24bd7c7db44df8b771843bbf7a14d1ea97656d85f1637bc6b037
-  data.tar.gz: 3c07cee9ec91029b06efcd2edd4b7528df2555fb6b8d33a6e4782a9e8521eef6a15553b54b0f6005ea529d3877336d37234dc5fc82da533641796b2cc7ca25a5
+  metadata.gz: 6e712abd3e2cdea918dd30cfdd8590fbfba8dfaa89b7546030202f14de79520233246cde85cbae9ecce432afda8f16f7ada45b9a770fb86d0be0692a27ea15e9
+  data.tar.gz: a8ae0f8fd73f91cf14b920732b1c7b1bf6c5a7f551069f53aca3e79299e7afa9bc6c4799f5bd7f1580cba6927de957ecc622b349b1a609a614813b79e9ad694d

data/README.md

@@ -2,7 +2,7 @@
 [![forthebadge](https://forthebadge.com/images/badges/made-with-ruby.svg)](https://www.ruby-lang.org/en/)
 [![Gem Version](https://badge.fury.io/rb/bioroebe.svg)](https://badge.fury.io/rb/bioroebe)
 
-This gem was <b>last updated</b> on the <span style="color: darkblue; font-weight: bold">22.02.2024</span> (dd.mm.yyyy notation), at <span style="color: steelblue; font-weight: bold">13:34:05</span> o'clock.
+This gem was <b>last updated</b> on the <span style="color: darkblue; font-weight: bold">09.04.2024</span> (dd.mm.yyyy notation), at <span style="color: steelblue; font-weight: bold">21:22:36</span> o'clock.
 
 # The Bioroebe Project
 

data/doc/todo/bioroebe_todo.md

@@ -1,4 +1,28 @@
 --------------------------------------------------------------------------------
+https://pepdraw.com/
+^^^ integrate this
+--------------------------------------------------------------------------------
+     W   D   E   N   N   M
+NH2-Trp-Asp-Glu-Asn-Asn-Met-COOH
+
+Nach dem genetischen Code wird dieses Hexa-
+peptid von folgender DNA-Sequenz codiert:
+
+  to_aa TGG-GAT-GAA-AAT-AAT-ATG
+  to_aa TGG-GAC-GAG-AAC-AAC-ATG
+  
+to_codon   W   D   E   N   N   M
+    
+^^^^ bioroebe: show_all_codons from commandline
+AND document this also in the doc
+es also 16 Oligonucleotide,
+welche die Sequenz Trp-Asp-Glu-Asn-Asn-Met
+codieren.
+
+deduce WDENNM 
+^^^^ show all of them!!!!
+^aka show ALL possible codons
+--------------------------------------------------------------------------------
 add support for
 
 class Cell

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

@@ -162,13 +162,6 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
 
   $VERBOSE = OLD_VERBOSE_VALUE # Reinstate the old verbosity level here.
 
-  # ========================================================================= #
-  # === one_to_three
-  # ========================================================================= #
-  def one_to_three(i)
-    ::Bioroebe.one_to_three(i)
-  end
-
   # ========================================================================= #
   # === extract                                                 (extract tag)
   #
@@ -677,4 +670,13 @@ class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
     opnn; erev i
   end; alias opne opnerev # === opne
 
+  # ========================================================================= #
+  # === one_to_three
+  #
+  # Delegate towards Bioroebe.one_to_three().
+  # ========================================================================= #
+  def one_to_three(i)
+    ::Bioroebe.one_to_three(i)
+  end
+
 end; end

data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb

@@ -113,6 +113,9 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     when :be_quiet
       be_quiet
       run_already = DEFAULT_RUN_MODE
+    # ======================================================================= #
+    # === :do_not_run_yet
+    # ======================================================================= #
     when :do_not_run_yet
       run_already = false
     end
@@ -126,6 +129,10 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     super()
     set_use_frame_number(:one) # Default is reading frame number one.
     # ======================================================================= #
+    # === :use_a_spacer_between_the_aminoacids
+    # ======================================================================= #
+    @internal_hash[:use_a_spacer_between_the_aminoacids] = false
+    # ======================================================================= #
     # === @codon_table_dataset
     #
     # Obtain the codon table dataset next.
@@ -170,6 +177,13 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     @internal_hash[:colourize_stop_codons] = true
   end
 
+  # ========================================================================= #
+  # === use_a_spacer_between_the_aminoacids?
+  # ========================================================================= #
+  def use_a_spacer_between_the_aminoacids?
+    @internal_hash[:use_a_spacer_between_the_aminoacids]
+  end
+
   # ========================================================================= #
   # === colourize_stop_codons?
   # ========================================================================= #
@@ -299,16 +313,25 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
        alias set_sequence       set_result # === use_this_sequence=
 
   # ========================================================================= #
-  # === report
+  # === do_show_this_reading_frame_header
+  # ========================================================================= #
+  def do_show_this_reading_frame_header(
+      i = @use_frame_number
+    )
+    e
+    coloured_frame = palegreen(
+      'frame-'+one_two_or_three(i)
+    )+rev
+    e "#{rev}The #{coloured_frame}#{rev} sequence is: (#{sequence?.size} aminoacids)"
+    e
+  end
+
+  # ========================================================================= #
+  # === report                                                   (report tag)
   # ========================================================================= #
   def report
     if be_verbose?
-      e
-      coloured_frame = palegreen(
-        'frame-'+one_two_or_three(@use_frame_number)
-      )+rev
-      e "#{rev}The #{coloured_frame}#{rev} sequence is: (#{sequence?.size} aminoacids)"
-      e
+      do_show_this_reading_frame_header(@use_frame_number)
     end
     do_report_the_reading_frame
   end
@@ -327,11 +350,15 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     if show_as_three_letter_aminoacid_sequence?
       i = one_to_three(i)
     end
+    if use_a_spacer_between_the_aminoacids?
+      splitted = i.split(//)
+      i = splitted.join('-')
+    end
     result = "#{lightgreen(i)}#{rev}"
     if colourize_stop_codons? and result.include?('*')
       result = result.dup if result.frozen?
       # ===================================================================== #
-      # Colourize stop codons in orchid. 
+      # Colourize stop codons in orchid colour. 
       # ===================================================================== #
       result.gsub!(
         /\*/,
@@ -391,26 +418,39 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     else
       case i
       # ===================================================================== #
-      # === Show a helpful ruler
+      # === Use a spacer token
+      #
+      # The default spacer token will be '-'.
       #
       # Usage example:
       #
-      #   dnatoaminoacidsequence AUGUUU --ruler
+      #   dnatoaminoacidsequence ATGGCCGAGATTGTGCTGGAGCACGTCAACAAGAAT --spacer
       #
       # ===================================================================== #
-      when /^-?-?ruler$/i
-        do_show_ruler
+      when /^-?-?3(-|_| )?spacer$/i,
+           /^-?-?spacer$/i
+        @internal_hash[:use_a_spacer_between_the_aminoacids] = true
       # ===================================================================== #
       # === Show the aminoacids as three-letter code
       #
       # Usage example:
       #
-      #   dnatoaminoacidsequence AUGUUU --three-letter
+      #   dnatoaminoacidsequence AUGUUUAAGCCGAAA --three-letter
       #
       # ===================================================================== #
       when /^-?-?three(-|_| )?letter$/i
         do_show_as_the_three_letter_aminoacid_sequence
       # ===================================================================== #
+      # === Show a helpful ruler
+      #
+      # Usage example:
+      #
+      #   dnatoaminoacidsequence AUGUUU --ruler
+      #
+      # ===================================================================== #
+      when /^-?-?ruler$/i
+        do_show_ruler
+      # ===================================================================== #
       # === Show the help section
       #
       # Usage example:

data/lib/bioroebe/electron_microscopy/parse_coordinates.rb

@@ -65,6 +65,13 @@ class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::Elec
     clear_coordinates
   end
 
+  # ========================================================================= #
+  # === clear_coordinates
+  # ========================================================================= #
+  def clear_coordinates
+    @array_coordinates = []
+  end
+
   # ========================================================================= #
   # === dataset?
   # ========================================================================= #
@@ -82,7 +89,7 @@ class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::Elec
     i = DEFAULT_FILE if i.nil?
     i = i.to_s.dup
     if be_verbose?
-      opnn; e "Next assigning to the file #{sfile(i)}."
+      opne "#{rev}Next assigning to the file #{sfile(i)}#{rev}."
     end
     @file = i
   end
@@ -139,17 +146,10 @@ class ParseCoordinates < ::Bioroebe::CommandlineApplication # === Bioroebe::Elec
       opnerev 'no file at `'+sfile(_)+'`.'
     else
       opnerev "We have #{sfancy(@array_coordinates.size.to_s)} "\
-              "coordinates in #{sfile(_)}."
+              "#{rev}coordinates in #{sfile(_)}#{rev}."
     end
   end
 
-  # ========================================================================= #
-  # === clear_coordinates
-  # ========================================================================= #
-  def clear_coordinates
-    @array_coordinates = []
-  end
-
   # ========================================================================= #
   # === determine_coordinates
   # ========================================================================= # 

data/lib/bioroebe/fasta_and_fastq/download_fasta.rb

@@ -68,7 +68,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
     _ = log_dir?
     if !(return_pwd == _)
       if be_verbose
-        opnn; e "Now changing directory to `#{sdir(_)}`."
+        opne "#{rev}Now changing directory to `#{sdir(_)}#{rev}`."
       end
       unless File.exist? _
         mkdir(_)
@@ -134,7 +134,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
         url.include?('&id=WP_')
         match = url
       else
-        opnn; e "We will use the URL `#{simp(url)}`"
+        opne "#{rev}We will use the URL `#{simp(url)}#{rev}`"
         remote_file_content = ''.dup # Our variable.
         # =================================================================== #
         # We store the content of the remote page in the variable called
@@ -164,7 +164,7 @@ class DownloadFasta < ::Bioroebe::CommandlineApplication # === Bioroebe::Downloa
             end 
           end
         rescue Errno::ENOENT => error
-          opnn; e tomato('We encountered an error, which we will feedback next.')
+          opne tomato('We encountered an error, which we will feedback next.')
           pp error
           match = url
         end

data/lib/bioroebe/ncbi/efetch.rb

@@ -143,7 +143,7 @@ class Ncbi < ::Bioroebe::Base
     if target_id.start_with? 'http'
       use_this_url = target_id.dup
     elsif target_id.to_s.empty?
-      opnn; e 'No target id was passed. Please provide an ID.'
+      opne 'No target id was passed. Please provide an ID.'
       exit
     else
       target_id = target_id.to_s
@@ -176,7 +176,7 @@ class Ncbi < ::Bioroebe::Base
       end
     end
     opnn; ::Bioroebe.erev 'We will use the following url: '
-    opnn; e "  #{::Colours.simp(use_this_url)}"
+    opne "  #{::Colours.simp(use_this_url)}"
     # ======================================================================= #
     # Go to our log-directory.
     # ======================================================================= #

data/lib/bioroebe/string_matching/hamming_distance.rb

@@ -143,12 +143,12 @@ class HammingDistance < ::Bioroebe::CommandlineApplication
       notify_the_user = true if input?.empty?
     end
     if notify_the_user
-      opnn; e 'Please provide input.'
-      opnn; e
-      opnn; e 'The two strings should be separated by a " ". Example:'
-      opnn; e
-      opnn; e simp('  AGUUCGAUGGAAAAT AGUCCGGUCGAAAAA')
-      opnn; e
+      opne 'Please provide input.'
+      opne
+      opne 'The two strings should be separated by a " ". Example:'
+      opne
+      opne simp('  AGUUCGAUGGAAAAT AGUCCGGUCGAAAAA')
+      opne
       return
     end
   end

data/lib/bioroebe/taxonomy/interactive.rb

@@ -723,13 +723,15 @@ class Interactive < ::Bioroebe::CommandlineApplication # === Bioroebe::Taxonomy:
   # ========================================================================= #
   # === create_dirs
   # ========================================================================= #
-  def create_dirs(be_verbose = false)
+  def create_dirs(
+      be_verbose = false
+    )
     case be_verbose
     when :be_verbose
       be_verbose = true
     end
     if be_verbose
-      opnn; e 'We will create the temp directory and the download directory next.'
+      opne 'We will create the temp directory and the download directory next.'
     end
     ensure_that_temp_dir_exists
     ensure_that_download_dir_exists

data/lib/bioroebe/toplevel_methods/toplevel_methods.rb

@@ -1145,29 +1145,6 @@ EOF
     return result
   end
 
-  # ========================================================================= #
-  # === Bioroebe.one_to_three
-  #
-  # This method will convert from the one-aminoacid letter to the
-  # three-letter code.
-  #
-  # Usage example:
-  #
-  #   Bioroebe.one_to_three('HIM') # => "His-Ile-Met"
-  #
-  # ========================================================================= #
-  def self.one_to_three(i)
-    if i.is_a? Array
-      i = i.join
-    end
-    inverted_hash = AMINO_ACIDS_THREE_TO_ONE.invert
-    chars = i.chars
-    result = chars.map {|one_aminoacid_letter|
-      inverted_hash[one_aminoacid_letter].capitalize+'-'
-    }.join
-    return result.chop
-  end
-
   # ========================================================================= #
   # === Bioroebe.weight_of_this_aminoacid?
   #
@@ -4409,6 +4386,42 @@ EOF
     esystem "wget #{target}"
   end
 
+  # ========================================================================= #
+  # === Bioroebe.edit_C_to_U
+  #
+  # This method attempts to do a RNA editing job, such as may be done in
+  # mitochondrial DNA.
+  #
+  # Usage examples:
+  #
+  #   Bioroebe.edit_C_to_U('AGG-GGU-GCU-UCG-GAU-CGG-GAG')                  # => "AGGGGUGUUUUGGAUUGGGAG"
+  #   Bioroebe.edit_C_to_U('AGG-GGU-GCU-UCG-GAU-CGG-GAG', :retain_hyphens) # => "AGG-GGU-GUU-UUG-GAU-UGG-GAG"
+  #   Bioroebe.to_aa(Bioroebe.edit_C_to_U('AGG-GGU-GCU-UCG-GAU-CGG-GAG', false)) # => "AGG-GGU-GUU-UUG-GAU-UGG-GAG")
+  #
+  # ========================================================================= #
+  def self.edit_C_to_U(
+      of_this_sequence,
+      retain_hyphens = false
+    )
+    case retain_hyphens
+    # ======================================================================= #
+    # === :retain_hyphens
+    # ======================================================================= #
+    when :retain_hyphens
+      retain_hyphens = true
+    end
+    if of_this_sequence.is_a? Array
+      of_this_sequence = of_this_sequence.first
+    end
+    if of_this_sequence.frozen?
+      of_this_sequence = of_this_sequence.dup
+    end
+    unless retain_hyphens
+      of_this_sequence.delete!('-') if of_this_sequence.include? '-'
+    end
+    of_this_sequence.tr('C','U')
+  end
+
   # ========================================================================= #
   # === Bioroebe.download
   # ========================================================================= #
@@ -5105,6 +5118,32 @@ EOF
     x # Return the cost here.
   end
 
+  # ========================================================================= #
+  # === Bioroebe.one_to_three
+  #
+  # This method will convert from the one-aminoacid letter to the
+  # three-letter code.
+  #
+  # Usage example:
+  #
+  #   Bioroebe.one_to_three('HIM') # => "His-Ile-Met"
+  #
+  # ========================================================================= #
+  def self.one_to_three(
+      i,
+      use_this_as_join_token = '-' # Or it could be empty, for no-join token.
+    )
+    if i.is_a? Array
+      i = i.join
+    end
+    inverted_hash = AMINO_ACIDS_THREE_TO_ONE.invert
+    chars = i.chars
+    result = chars.map {|one_aminoacid_letter|
+      "#{inverted_hash[one_aminoacid_letter].capitalize}#{use_this_as_join_token}"
+    }.join
+    return result.chop
+  end
+
 end
 
 if __FILE__ == $PROGRAM_NAME

data/lib/bioroebe/version/version.rb

@@ -9,7 +9,7 @@ module Bioroebe
   # ========================================================================= #
   # === VERSION
   # ========================================================================= #
-  VERSION = '0.13.31'
+  VERSION = '0.13.32'
 
   # ========================================================================= #
   # === 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 = '22.02.2024'
+  LAST_UPDATE = '09.04.2024'
 
   # ========================================================================= #
   # === URL_TO_THE_DOCUMENTATION

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bioroebe
 version: !ruby/object:Gem::Version
-  version: 0.13.31
+  version: 0.13.32
 platform: ruby
 authors:
 - Robert A. Heiler
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2024-02-22 00:00:00.000000000 Z
+date: 2024-04-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: chemistry_paradise
@@ -954,7 +954,7 @@ post_install_message: |2+
 
   For more documentation, have a look at:
 
-    https://www.rubydoc.info/gems/bioroebe/0.13.31
+    https://www.rubydoc.info/gems/bioroebe/0.13.32
 
 rdoc_options: []
 require_paths:
@@ -968,9 +968,9 @@ required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 3.5.6
+      version: 3.5.7
 requirements: []
-rubygems_version: 3.5.6
+rubygems_version: 3.5.7
 signing_key:
 specification_version: 4
 summary: 'This is the bioroebe-0.13.x release series. It is encouraged to use ruby