bioroebe 0.10.80

data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb

@@ -0,0 +1,471 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/utility_scripts/display_open_reading_frames/misc.rb'
+# =========================================================================== #
+module Bioroebe
+
+class DisplayOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe::DisplayOpenReadingFrames
+
+  # ========================================================================= #
+  # === set_dna_sequence
+  # ========================================================================= #
+  def set_dna_sequence(
+      i = @commandline_arguments.first
+    )
+    i = i.to_s.dup # We always want a free, unfrozen sequence here.
+    # ======================================================================= #
+    # We also allow reading for some files, e. g. "foobar.fasta" and similar
+    # variants.
+    # ======================================================================= #
+    if i and i.include?('.') and File.file?(i)
+      i = File.read(i).strip
+    end 
+    @dna_sequence = i
+  end
+
+  # ========================================================================= #
+  # === dna_sequence?
+  # ========================================================================= #
+  def dna_sequence?
+    @dna_sequence
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    menu
+    _ = dna_sequence?
+    reverse_dna_strand = complementary_dna_strand(_)
+    determine_all_six_reading_frames(_, reverse_dna_strand)
+    show_the_intro_for_this_class
+    e
+    chunks = dna_sequence?.scan(/.{1,#{n_nucleotides_per_line?}}/)
+    chunks.each_with_index {|this_sequence, index| index += 1
+      this_sequence = this_sequence.dup
+      if this_sequence.size > 2
+        show_frame3( Bioroebe.to_aa(this_sequence[2 .. -1]) )
+        show_frame2( Bioroebe.to_aa(this_sequence[1 .. -1]) )
+        show_frame1( Bioroebe.to_aa(this_sequence) )
+      end
+      show_top_sequence(this_sequence, index * @split_at_n_characters)
+      if this_sequence.size > 2
+        display_modulo_ten_spacer
+        central_part(this_sequence.size)
+        if @display_reverse_frames
+          display_modulo_ten_spacer(
+            this_sequence, :reverse, padding_to_use?[0, (padding_to_use?.size - 10)]
+          )
+          display_the_nucleotide_sequence_on_bottom(
+            complementary_dna_strand(this_sequence)
+          )
+          display_reverse_frame1(Bioroebe.to_aa(complement(this_sequence).reverse))
+          display_reverse_frame2(Bioroebe.to_aa(complement(this_sequence).reverse[1..-1]))
+          display_reverse_frame3(Bioroebe.to_aa(complement(this_sequence).reverse[2..-1]))
+        end
+      end
+      e # Make a newline after each chunked display.
+    }
+    e
+    report_the_start_codons_and_the_stop_codons_in_use
+    e
+    report_how_many_ORFs_are_found
+  end
+
+  # ========================================================================= #
+  # === frame1?
+  # ========================================================================= #
+  def frame1?
+    @hash[:frame1]
+  end
+
+  # ========================================================================= #
+  # === frame2?
+  # ========================================================================= #
+  def frame2?
+    @hash[:frame2]
+  end
+
+  # ========================================================================= #
+  # === frame4?
+  # ========================================================================= #
+  def frame4?
+    @hash[:reverse_frame1]
+  end
+
+  # ========================================================================= #
+  # === frame5?
+  # ========================================================================= #
+  def frame5?
+    @hash[:reverse_frame2]
+  end
+
+  # ========================================================================= #
+  # === frame6?
+  # ========================================================================= #
+  def frame6?
+    @hash[:reverse_frame3]
+  end
+
+  # ========================================================================= #
+  # === frame3?
+  # ========================================================================= #
+  def frame3?
+    @hash[:frame3]
+  end
+
+  # ========================================================================= #
+  # === colourized_frame1
+  # ========================================================================= #
+  def colourized_frame1
+    orange(' F1 ')
+  end
+
+  # ========================================================================= #
+  # === colourized_frame2
+  # ========================================================================= #
+  def colourized_frame2
+    orange(' F2 ')
+  end
+
+  # ========================================================================= #
+  # === colourized_frame3
+  # ========================================================================= #
+  def colourized_frame3
+    orange(' F3 ')
+  end
+
+  # ========================================================================= #
+  # === colourized_reverse_frame1
+  # ========================================================================= #
+  def colourized_reverse_frame1
+    orangered(' R1 ')
+  end
+
+  # ========================================================================= #
+  # === colourized_reverse_frame2
+  # ========================================================================= #
+  def colourized_reverse_frame2
+    orangered(' R2 ')
+  end
+
+  # ========================================================================= #
+  # === colourized_reverse_frame3
+  # ========================================================================= #
+  def colourized_reverse_frame3
+    orangered(' R3 ')
+  end
+
+  # ========================================================================= #
+  # === two_spaces_padding
+  # ========================================================================= #
+  def two_spaces_padding(i, modify_the_padding_by_this = 0)
+    padding_to_use = @split_at_n_characters
+    padding_to_use += modify_the_padding_by_this
+    splitted = i.split(//)
+    result = splitted.map {|entry| "#{entry}  " }.join.strip.ljust(padding_to_use)
+    return result
+  end
+
+  # ========================================================================= #
+  # === colourize_this_aminoacid_sequence
+  # ========================================================================= #
+  def colourize_this_aminoacid_sequence(i)
+    result = olivedrab(i).dup
+    if @colourize_the_stop_codons
+      result.gsub!(/\*/, orangered('*')+
+        ::Colours.remove_trailing_ansii_escape_code(
+          olivedrab('')
+        )
+      )
+    end
+    result
+  end
+
+  # ========================================================================= #
+  # === display_the_three_regular_frames
+  # ========================================================================= #
+  def display_the_three_regular_frames
+    show_frame3
+    show_frame2
+    show_frame1
+  end
+
+  # ========================================================================= #
+  # === display_separator_in_the_middle                          (middle tag)
+  #
+  # This method will display the separator in the middle.
+  # ========================================================================= #
+  def display_separator_in_the_middle(
+      display_n_nucleotides = display_n_nucleotides?
+    )
+    _ = ('-' * display_n_nucleotides).dup
+    _.gsub!(/----------/, '---------|')
+    _.gsub!(/---------/, seagreen('---------'))
+    _.gsub!(/\|/, palegreen('|')+
+                  ::Colours.remove_trailing_ansii_escape_code(
+                    seagreen('')
+                  )
+           )
+    e "#{@left_padding}#{_}"
+  end; alias central_part display_separator_in_the_middle # === central_part
+
+  # ========================================================================= #
+  # === show_frame3
+  # ========================================================================= #
+  def show_frame3(
+      i = frame3?
+    )
+    e @left_padding+'  '+
+      colourize_this_aminoacid_sequence(two_spaces_padding(i, -2))+
+      colourized_frame3
+  end
+
+  # ========================================================================= #
+  # === show_frame2
+  # ========================================================================= #
+  def show_frame2(
+      i = frame2?
+    )
+    e @left_padding+' '+
+      colourize_this_aminoacid_sequence(two_spaces_padding(i, -1))+
+      colourized_frame2
+  end
+
+  # ========================================================================= #
+  # === show_frame1
+  # ========================================================================= #
+  def show_frame1(
+      i = frame1?
+    )
+    e @left_padding+
+      colourize_this_aminoacid_sequence(two_spaces_padding(i))+
+      colourized_frame1
+  end
+
+  # ========================================================================= #
+  # === display_the_nucleotide_sequence_on_top                      (top tag)
+  #
+  # The second argument shows at which number this method will stop.
+  # ========================================================================= #
+  def display_the_nucleotide_sequence_on_top(
+      i           = dna_sequence?,
+      upper_range = display_n_nucleotides_per_line?
+    )
+    min_number = (upper_range - @split_at_n_characters)+1
+    padding_to_use = @left_padding.dup
+    (min_number.to_s.size + 1).times { padding_to_use.chop! }
+    if upper_range > i.size
+      upper_range = i.size+(min_number-1)
+    end
+    e padding_to_use+
+      paleturquoise(
+        min_number.to_s+' '
+      )+
+      steelblue(i)+ # ← This is the nucleotide sequence that is to be shown.
+      ' '+
+      paleturquoise(upper_range.to_s)+ # ← This will be shown on the right hand side.
+      steelblue(' →')
+  end; alias show_top_sequence display_the_nucleotide_sequence_on_top # === show_top_sequence
+
+  # ========================================================================= #
+  # === display_reverse_frame1
+  # ========================================================================= #
+  def display_reverse_frame1(i = @hash[:reverse_frame1].reverse)
+    modify_the_padding = 0
+    n_characters = i.size * 3
+    if n_characters < threshold_value?
+      modify_the_padding = -(threshold_value? - n_characters)
+    end
+    # ======================================================================= #
+    # === Reverse frame 1
+    # ======================================================================= #
+    result = @left_padding+
+             colourize_this_aminoacid_sequence(
+               two_spaces_padding_last(
+                 i.reverse, modify_the_padding
+               )
+             ).dup
+    if modify_the_padding < 0
+      result << ' ' * modify_the_padding.abs
+    end
+    e result+
+      colourized_reverse_frame1
+  end
+
+  # ========================================================================= #
+  # === display_reverse_frame2
+  # ========================================================================= #
+  def display_reverse_frame2(i = @hash[:reverse_frame2].reverse)
+    modify_the_padding = 0
+    n_characters = i.size * 3
+    if n_characters < threshold_value?
+      modify_the_padding = -(threshold_value? - n_characters)
+    end
+    # ======================================================================= #
+    # === Reverse frame 2
+    # ======================================================================= #
+    _ = two_spaces_padding_last(i, modify_the_padding)
+    result = @left_padding+
+             colourize_this_aminoacid_sequence(
+               _.reverse
+             ).dup
+    if modify_the_padding < 0
+      result << ' ' * modify_the_padding.abs
+    end
+    e result+
+      colourized_reverse_frame2
+  end
+
+  # ========================================================================= #
+  # === display_reverse_frame3
+  # ========================================================================= #
+  def display_reverse_frame3(i = @hash[:reverse_frame3].reverse)
+    modify_the_padding = 0
+    n_characters = (i.size * 3) - 2
+    if n_characters < threshold_value?
+      modify_the_padding = -(threshold_value? - n_characters)
+    end
+    # ======================================================================= #
+    # === Reverse frame 3
+    # ======================================================================= #
+    _ = two_spaces_padding_last(i, modify_the_padding)
+    result = @left_padding+
+             colourize_this_aminoacid_sequence(
+               _.reverse
+             ).dup
+    if modify_the_padding < 0
+      result << ' ' * modify_the_padding.abs
+    end
+    e result+
+      colourized_reverse_frame3
+  end
+
+  # ========================================================================= #
+  # === two_spaces_padding_last
+  # ========================================================================= #
+  def two_spaces_padding_last(
+      i, modify_the_padding_by_this = 0
+    )
+    padding_to_use = @split_at_n_characters
+    padding_to_use += modify_the_padding_by_this
+    splitted = i.split(//)
+    result = splitted.map {|entry|
+      "  #{entry}"
+    }.join.strip.rjust(padding_to_use)
+    return result
+  end
+
+  # ========================================================================= #
+  # === set_split_at_n_characters
+  # ========================================================================= #
+  def set_split_at_n_characters(i)
+    @split_at_n_characters = i.to_i
+  end; alias set_threshold set_split_at_n_characters # === set_threshold
+
+  # ========================================================================= #
+  # === left_padding?
+  # ========================================================================= #
+  def left_padding?
+    @left_padding
+  end; alias padding_to_use? left_padding? # === padding_to_use?
+
+  # ========================================================================= #
+  # === colourize_dna
+  # ========================================================================= #
+  def colourize_dna(i)
+    paleturquoise(i)
+  end
+
+  # ========================================================================= #
+  # === display_modulo_ten_spacer
+  #
+  # This method will display the "   10   20" spacer. We have to make
+  # sure that there are not more of these rulers shown than there
+  # are n characters in the sequence that is to be displayed, in order
+  # to avoid an overflow.
+  #
+  # If the argument is :reverse then this method will count downwards
+  # rather than upwards.
+  # ========================================================================= #
+  def display_modulo_ten_spacer(
+      sequence_to_use  = dna_sequence?,
+      optional_mode    = :normal,
+      use_this_padding = @left_padding
+    )
+    spacer = replace_this_input_with_modulo_ten(
+               sequence_to_use,
+               '-' * n_nucleotides,
+               optional_mode
+             )
+    result = use_this_padding+spacer
+    e result
+  end
+
+  # ========================================================================= #
+  # === split_at_n_characters?
+  # ========================================================================= #
+  def split_at_n_characters?
+    @split_at_n_characters
+  end; alias display_n_nucleotides_per_line? split_at_n_characters? # === display_n_nucleotides_per_line?
+       alias display_n_nucleotides?          split_at_n_characters? # === display_n_nucleotides?
+       alias n_nucleotides_per_line?         split_at_n_characters? # === n_nucleotides_per_line?
+       alias n_nucleotides?                  split_at_n_characters? # === n_nucleotides?
+       alias n_nucleotides                   split_at_n_characters? # === n_nucleotides
+       alias threshold_value?                split_at_n_characters? # === threshold_value?
+
+  # ========================================================================= #
+  # === replace_this_input_with_modulo_ten
+  # ========================================================================= #
+  def replace_this_input_with_modulo_ten(
+      sequence_to_use = dna_sequence?,
+      i               = '-' * n_nucleotides?,
+      optional_mode   = :default
+    )
+    result = ''.dup
+    index = 0
+    max_number = split_at_n_characters?
+    # ======================================================================= #
+    # Next deduct from this number if there are fewer characters in the
+    # target sequence.
+    # ======================================================================= #
+    if max_number > (dna_sequence?.size + 5) # We add +5 as a "grace" boundary.
+      max_number = dna_sequence?.size + 5
+    end 
+    i.chars.each {|this_char| index += 1
+      unless index > max_number
+        if (index % 10 == 0)
+          # =================================================================== #
+          # In this case we must add the correct number.
+          # =================================================================== #
+          _ = index
+          if optional_mode == :reverse
+            _ = (( max_number + 10 ) - index).to_s
+          end
+          result << _.to_s
+        else
+          if (index > 10) and (index % 10 == 1)
+          else
+            result << ' '
+          end
+        end
+      end
+    }
+    case optional_mode
+    when :reverse
+      result << (' ' * 10)
+    end
+    # ======================================================================= #
+    # Next honour the size-restriction, if there is one.
+    # ======================================================================= #
+    # if (optional_mode == :reverse) and (sequence_to_use.size < threshold_value?)
+    #   result << ' ' * (threshold_value? - sequence_to_use.size)
+    #   result[0, (threshold_value? - sequence_to_use.size)] = ''
+    # end
+    result = mediumseagreen(result)
+    return result
+  end
+
+end; end

data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb

@@ -0,0 +1,113 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/utility_scripts/display_open_reading_frames/report.rb'
+# =========================================================================== #
+module Bioroebe
+
+class DisplayOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe::DisplayOpenReadingFrames
+
+  # ========================================================================= #
+  # === show_the_intro_for_this_class
+  # ========================================================================= #
+  def show_the_intro_for_this_class
+    e
+    erev "Translation of requested code (5' "+
+         steelblue('→')+
+         rev+" 3') for "+
+         colourize_dna(
+           dna_sequence?.size.to_s
+         )+
+         rev+' nucleotides.'
+    e
+    e '  '+orange('F1')+rev+', '+orange('F2')+rev+
+      ' and '+orange('F3')+rev+
+      ' designates the three forward reading frames.'
+    if @display_reverse_frames
+      e '  '+
+        orangered('R1')+rev+', '+
+        orangered('R2')+
+        rev+
+        ' and '+
+        orangered('R3')+
+        rev+
+        ' designates the three reverse reading frames.'
+    end
+    e
+  end
+
+  # ========================================================================= #
+  # === display_the_nucleotide_sequence_on_bottom
+  # ========================================================================= #
+  def display_the_nucleotide_sequence_on_bottom(
+      i = complementary_dna_strand(dna_sequence?)
+    )
+    e (@left_padding.chop.chop.chop.chop.chop)+
+      steelblue('← ')+
+      paleturquoise(
+        (display_n_nucleotides_per_line? + 1).to_s
+      )+
+      ' '+
+      steelblue(i)+
+      paleturquoise(' 1')
+  end
+
+  # ========================================================================= #
+  # === report_how_many_ORFs_are_found
+  # ========================================================================= #
+  def report_how_many_ORFs_are_found
+    n_ORFs_in_total = 0
+    n_ORFs_in_total += (n_ORFs_in_frame1 = return_n_ORFs_in_this_sequence(frame1?))
+    n_ORFs_in_total += (n_ORFs_in_frame2 = return_n_ORFs_in_this_sequence(frame2?))
+    n_ORFs_in_total += (n_ORFs_in_frame3 = return_n_ORFs_in_this_sequence(frame3?))
+    n_ORFs_in_total += (n_ORFs_in_frame4 = return_n_ORFs_in_this_sequence(frame4?))
+    n_ORFs_in_total += (n_ORFs_in_frame5 = return_n_ORFs_in_this_sequence(frame5?))
+    n_ORFs_in_total += (n_ORFs_in_frame6 = return_n_ORFs_in_this_sequence(frame6?))
+    e
+    erev 'Total ORFs in frame 1, frame 2, frame 3: '+
+         steelblue(
+           n_ORFs_in_frame1.to_s+', '+
+           n_ORFs_in_frame2.to_s+', '+
+           n_ORFs_in_frame3.to_s
+         )
+    erev 'Total ORFs in frame 4, frame 5, frame 6: '+
+         steelblue(
+           n_ORFs_in_frame4.to_s+', '+
+           n_ORFs_in_frame5.to_s+', '+
+           n_ORFs_in_frame6.to_s
+         )
+    e
+    erev 'Total ORFs in that sequence: '+
+          steelblue(n_ORFs_in_total.to_s)
+    e
+  end
+
+  # ========================================================================= #
+  # === report_the_start_codons_and_the_stop_codons_in_use
+  # ========================================================================= #
+  def report_the_start_codons_and_the_stop_codons_in_use
+    start_codons_in_use = Bioroebe.start_codons?
+    if start_codons_in_use.size > 1
+      _ = 'The start codons in use were: '.ljust(30)
+    else
+      _ = 'The start codons in use was: '.ljust(30)
+    end
+    erev _+
+         royalblue(
+           start_codons_in_use.join(' ')
+         )
+    erev 'The stop codons were: '.ljust(30)+
+         royalblue(
+           Bioroebe.stop_codons?.join(' ')
+         )
+  end
+
+  # ========================================================================= #
+  # === return_n_ORFs_in_this_sequence
+  # ========================================================================= #
+  def return_n_ORFs_in_this_sequence(i)
+    ::Bioroebe.return_n_ORFs_in_this_sequence(i)
+  end
+
+end; end

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

@@ -0,0 +1,56 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/utility_scripts/display_open_reading_frames/reset.rb'
+# =========================================================================== #
+module Bioroebe
+
+class DisplayOpenReadingFrames < ::Bioroebe::CommandlineApplication # === Bioroebe::DisplayOpenReadingFrames
+
+  # ========================================================================= #
+  # === reset
+  # ========================================================================= #
+  def reset
+    super()
+    if ::Bioroebe.stop_codons?.empty?
+      Bioroebe.initialize_stop_codons
+    end
+    # ======================================================================= #
+    # === @split_at_n_characters
+    #
+    # This variable determines our threshold, e. g. to split at n
+    # characters.
+    # ======================================================================= #
+    @split_at_n_characters = 60
+    # ======================================================================= #
+    # === @left_padding
+    #
+    # How much we will pad towards the left-side of the screen/display.
+    # ======================================================================= #
+    @left_padding = (' ' * 12)
+    # ======================================================================= #
+    # === @colourize_the_stop_codons
+    # ======================================================================= #
+    @colourize_the_stop_codons = true
+    # ======================================================================= #
+    # === @display_reverse_frames
+    #
+    # If true then both forward and reverse frames will be displayed.
+    # ======================================================================= #
+    @display_reverse_frames = true
+    # ======================================================================= #
+    # === @hash
+    #
+    # The following Hash will only keep the six different reading frames.
+    # ======================================================================= #
+    @hash = {}
+    @hash[:frame1] = nil
+    @hash[:frame2] = nil
+    @hash[:frame3] = nil
+    @hash[:reverse_frame1] = nil
+    @hash[:reverse_frame2] = nil
+    @hash[:reverse_frame3] = nil
+  end
+
+end; end