bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb

@@ -40,6 +40,7 @@ module Bioroebe
 class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe::DnaToAminoacidSequence
 
   require 'bioroebe/codons/codon_table.rb'
+  require 'bioroebe/misc/ruler.rb'
 
   # ========================================================================= #
   # === DEFAULT_RUN_MODE
@@ -63,8 +64,14 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     if block_given?
       yielded = yield
       case yielded
+      # ===================================================================== #
+      # === :be_verbose
+      # ===================================================================== #
       when :be_verbose
-        @be_verbose = true
+        set_be_verbose
+      # ===================================================================== #
+      # === :be_quiet
+      # ===================================================================== #
       when :be_quiet
         be_quiet
       end
@@ -140,27 +147,34 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     # ======================================================================= #
     @use_the_codon_table_for = :humans
     # ======================================================================= #
-    # === @colourize_stop_codons
-    #
-    # If the following variable is set to true then any stop codon, aka
-    # '*', will appear in the colour orchid.
-    # ======================================================================= #
-    @colourize_stop_codons = true
-    # ======================================================================= #
-    # === @internal_hash
-    # ======================================================================= #
-    @internal_hash = {}
-    # ======================================================================= #
     # === :report_result
     # ======================================================================= #
     @internal_hash[:report_result] = true
     # ======================================================================= #
+    # === :show_ruler
+    # ======================================================================= #
+    @internal_hash[:show_ruler] = false
+    # ======================================================================= #
     # === :show_as_three_letter_aminoacid_sequence
     #
     # If this is true then this class will show "Phe" rather than "F" for
     # that amino acid. The same is true for all the other aminoacids as well.
     # ======================================================================= #
     @internal_hash[:show_as_three_letter_aminoacid_sequence] = false
+    # ======================================================================= #
+    # === :colourize_stop_codons
+    #
+    # If the following variable is set to true then any stop codon, aka
+    # '*', will appear in the colour orchid.
+    # ======================================================================= #
+    @internal_hash[:colourize_stop_codons] = true
+  end
+
+  # ========================================================================= #
+  # === colourize_stop_codons?
+  # ========================================================================= #
+  def colourize_stop_codons?
+    @internal_hash[:colourize_stop_codons]
   end
 
   # ========================================================================= #
@@ -188,7 +202,7 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
   # === be_quiet
   # ========================================================================= #
   def be_quiet
-    @be_verbose = false
+    set_be_quiet
     @internal_hash[:report_result] = false
   end
 
@@ -205,10 +219,19 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
   # ========================================================================= #
   def one_two_or_three(i)
     case i
+    # ======================================================================= #
+    # === :frame_one
+    # ======================================================================= #
     when :frame_one
       '1'
+    # ======================================================================= #
+    # === :frame_two
+    # ======================================================================= #
     when :frame_two
       '2'
+    # ======================================================================= #
+    # === :frame_three
+    # ======================================================================= #
     when :frame_three
       '3'
     end
@@ -220,18 +243,28 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
   # Designate which frame is to be used through this method. By default
   # it will be frame number 1.
   # ========================================================================= #
-  def set_use_frame_number(i = :default)
+  def set_use_frame_number(
+      i = :default
+    )
     case i
     # ======================================================================= #
+    # === :one
+    #
     # First comes the default.
     # ======================================================================= #
     when :one,
          :default,
          '1'
       i = :frame_one
+    # ======================================================================= #
+    # === :two
+    # ======================================================================= #
     when :two,
          '2'
       i = :frame_two
+    # ======================================================================= #
+    # === :three
+    # ======================================================================= #
     when :three,
          '3'
       i = :frame_three
@@ -295,7 +328,7 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
       i = one_to_three(i)
     end
     result = "#{lightgreen(i)}#{rev}"
-    if @colourize_stop_codons and result.include?('*')
+    if colourize_stop_codons? and result.include?('*')
       result = result.dup if result.frozen?
       # ===================================================================== #
       # Colourize stop codons in orchid. 
@@ -307,7 +340,10 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
       )
     end
     set_result(result)
-    if report_result? and @be_verbose
+    if report_result? and be_verbose?
+      if show_ruler? # Show a pretty ruler here.
+        e "  #{Bioroebe.return_ruler(i)}"
+      end
       e "  #{@result}"
       e N
     end
@@ -339,23 +375,6 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     ]
   end
 
-  # ========================================================================= #
-  # === show_help                                                  (help tag)
-  # ========================================================================= #
-  def show_help
-    e 'Available options:'
-    e
-    e '  --gui                           # start the GUI'
-    e '  --stop-at-the-first-stop-codon  # stop at the first stop codon encountered'
-    e '  --frame1                        # show the first frame translation only'
-    e '  --frame2                        # show the second frame translation only'
-    e '  --frame3                        # show the third frame translation only'
-    e '  --use-this-codon-table=bacteria # specify a specific codon table '\
-      '(in this case bacteria)'
-    e '  --three-letter                  # show the three letter amino acid code'
-    e
-  end
-
   # ========================================================================= #
   # === menu                                                       (menu tag)
   #
@@ -372,6 +391,16 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     else
       case i
       # ===================================================================== #
+      # === Show a helpful ruler
+      #
+      # Usage example:
+      #
+      #   dnatoaminoacidsequence AUGUUU --ruler
+      #
+      # ===================================================================== #
+      when /^-?-?ruler$/i
+        do_show_ruler
+      # ===================================================================== #
       # === Show the aminoacids as three-letter code
       #
       # Usage example:
@@ -466,7 +495,9 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
     # Use the proper, designated codon-table.
     # ======================================================================= #
     ::Bioroebe.load_the_codon_table_dataset(@use_the_codon_table_for)
-    _ = first_argument?.dup
+    _ = ensure_DNA_sequence(
+      commandline_arguments?.join(' ').strip.dup.delete(' ').delete('-') # We don't want any "-" there.
+    )
     if _ and _.include?('.') and File.file?(_)
       _ = File.read(_).strip # Add support for reading local files here.
     end
@@ -496,14 +527,54 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
       #
       # The result is stored in the variable called @result.
       # ===================================================================== #
-      translated_codon = translate_dna_into_aminoacid(this_codon)
-      @result << translated_codon.to_s
+      translated_codon = translate_dna_into_aminoacid(this_codon).to_s
+      @result << translated_codon
       if @stop_at_the_first_stop_codon and (translated_codon == '*')
         break
       end
     }
   end
 
+  # ========================================================================= #
+  # === ensure_DNA_sequence
+  # ========================================================================= #
+  def ensure_DNA_sequence(i)
+    return i.tr('U','T')
+  end
+
+  # ========================================================================= #
+  # === show_help                                                  (help tag)
+  # ========================================================================= #
+  def show_help
+    e 'Available options:'
+    e
+    e '  --gui                           # start the GUI'
+    e '  --stop-at-the-first-stop-codon  # stop at the first stop codon encountered'
+    e '  --frame1                        # show the first frame translation only'
+    e '  --frame2                        # show the second frame translation only'
+    e '  --frame3                        # show the third frame translation only'
+    e '  --use-this-codon-table=bacteria # specify a specific codon table '\
+      '(in this case bacteria)'
+    e '  --three-letter                  # show the three letter amino acid code'
+    e '  --ruler                         # show a helpful ruler on top '\
+      'of the sequence'
+    e
+  end
+ 
+  # ========================================================================= #
+  # === do_show_ruler
+  # ========================================================================= #
+  def do_show_ruler
+    @internal_hash[:show_ruler] = true
+  end
+
+  # ========================================================================= #
+  # === show_ruler?
+  # ========================================================================= #
+  def show_ruler?
+    @internal_hash[:show_ruler]
+  end
+
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
@@ -516,7 +587,7 @@ class DnaToAminoacidSequence < ::Bioroebe::CommandlineApplication # === Bioroebe
   # ========================================================================= #
   # === Bioroebe::DnaToAminoacidSequence[]
   # ========================================================================= #
-  def self.[](i = '')
+  def self.[](i = ARGV)
     new(i) { :be_quiet }.result
   end
 
@@ -556,8 +627,7 @@ if __FILE__ == $PROGRAM_NAME
   if _.empty?
     _ = 'ATGCGTAAAGGAGAAGAACTTTTCACTTGGAGTTGTCCCAATTCTTGTTGGGAATTAGATGGTGATGTTAATGGGCACAAATTTTCTGTCAGTGGAGAGGGTGAAGGTGATGCAACATACGGAAAACTTACCCTTAAATTTATTTGCACTACTGGAAAACTACCTGTTCCATGGCCAACACTTGTCACTACTTTCGGTTATGGTGTTCAATGCTTTGCGAGATACCCAGATCATATGAAACAGCATGACTTTTTCAAGAGTGCCATGCCCGAAGGTTATGTACAGGAAAGAACTATATTTTTCAAAGATGACGGGAACTACAAGACACGTGCTGAAGTCAAGTTTGAAGGTGATACCCTTGTTAATAGAATCGAGTTAAAAGGTATTGATTTTAAAGAAGATGGAAACATTCTTGGACACAAATTGGAATACAACTATAACTCACACAATGTATACATCATGGCAGACAAACAAAAGAATGGAATCAAAGTTAACTTCAAAATTAGACACAACATTGAAGATGGAAGCGTTCAACTAGCAGACCATTATCAACAAAATACTCCAATTGGCGATGGCCCTGTCCTTTTACCAGACAACCATTACCTGTCCACACAATCTGCCCTTTCGAAAGATCCCAACGAAAAGAGAGACCACATGGTCCTTCTTGAGTTTGTAACAGCTGCTGGGATTACACATGGCATGGATGAACTATACAAATAG'
   end
-  Bioroebe.erev 'The input-sequence was: '+
-                 _.join
+  Bioroebe.erev('The input-sequence was: '+_)
   Bioroebe::DnaToAminoacidSequence.new(_)
   e
   e 'Next, all three frames will be translated:'

data/lib/bioroebe/count/count_amount_of_aminoacids.rb

@@ -143,7 +143,8 @@ class CountAmountOfAminoacids < ::Bioroebe::CommandlineApplication # === Bioroeb
     # ======================================================================= #
     if @be_verbose
       erev "This protein (#{yellow(n_members.to_s)}#{rev} aminoacids) has "\
-           "the following aminoacid composition (Frame 1)."; e
+           "#{olivedrab('the following aminoacid composition')}#{rev} "\
+           "(Frame 1)."; e
     end
     sorted = @hash.sort_by(&:first)
     sorted.each {|key, value|
@@ -158,7 +159,7 @@ class CountAmountOfAminoacids < ::Bioroebe::CommandlineApplication # === Bioroeb
         ') ('+name_of_the_aminoacid+')' if @be_verbose
     }
     if @be_verbose
-      report_how_many_aminoacids_we_have_found
+      report_how_many_aminoacids_we_have_found; e
       report_the_molecular_mass_of_these_aminoacids
       report_the_number_of_negatively_and_positively_charged_residues
       report_the_atomic_composition

data/lib/bioroebe/count/count_amount_of_nucleotides.rb

@@ -425,6 +425,9 @@ class CountAmountOfNucleotides < ::Bioroebe::CommandlineApplication # === Bioroe
     if File.exist? i.to_s
       i = File.read(i.to_s).strip.delete(N)
     end
+    if i.is_a? Array
+      i = i.join(' ').strip
+    end
     i = i.to_s.dup if i.frozen?
     i.upcase! # Want to keep it upcased.
     @dna_string = i

data/lib/bioroebe/cpp

@@ -0,0 +1 @@
+C++

data/lib/bioroebe/crystal/README.md

@@ -0,0 +1,2 @@
+This may contain experimental crystal support for the bioroebe
+project.

data/lib/bioroebe/crystal/to_rna.cr

@@ -0,0 +1,19 @@
+module Bioroebe
+
+  # ========================================================================= #
+  # === Bioroebe.to_rna
+  # ========================================================================= #
+  def self.to_rna(i = ARGV)
+    if i.is_a? Array
+      i = i.first?
+    end
+    if i.nil? || i.empty?
+      return i
+    else
+      return i.gsub("T","U")
+    end
+  end
+
+end
+
+puts Bioroebe.to_rna(ARGV)

data/lib/bioroebe/data/README.md

@@ -1,10 +1,13 @@
-This directory may contain some FASTA files or .pdb files, as
-that may be of help of people who end up using the BioRoebe
-project.
+This directory may contain some FASTA files or .pdb files, as that may 
+be of help of people who end up using the BioRoebe project.
+
+That dataset can be quickly tested and used to demonstrate how the 
+BioRoebe project works.
+
+In the pdb/ directory there is presently only one .pdb file. This 
+file is used mostly for a test .rb file in the test/ directory.
+
+The directory electron_microscopy/ is used primarily for cryo-electron
+microscopy and what not, using software such as relion.
 
-That dataset can be quickly tested and used to demonstrate how
-the BioRoebe project works.
 
-In the pdb/ directory there is presently only one .pdb file.
-This file is used mostly for a test .rb file in the test/
-directory.