Class: Bioroebe::DisplayOpenReadingFrames

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb,
lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb,
lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb,
lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb,
lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb,
lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb,
lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb

Overview

Bioroebe::DisplayOpenReadingFrames

Constant Summary

Constants inherited from CommandlineApplication

CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Instance Method Summary collapse

Methods inherited from CommandlineApplication

#all_aminoacids?, #append_what_into, #at_home?, #be_silent, #be_verbose?, #cat, #ccliner, #change_directory, #cliner, #codon_table_dataset?, #codon_to_aminoacid, #codons_for?, #colourize_this_dna_sequence, #complement, #cp, #disable_warnings, #download_dir?, #editor?, #enable_warnings, #ensure_that_the_base_directories_exist, #esystem, #extract, #is_this_a_start_codon?, #is_this_a_stop_codon?, #leading_five_prime, #load_bioroebe_yaml_file, #log_directory?, #one_letter_to_long_name, #one_to_three, #only_numbers?, #open_in_browser, #opnerev, #opnn, #pad_with_double_quotes, #pad_with_single_quotes, #partner_nucleotide, #remove_numbers, #remove_trailing_ansii_escape_code, #return_all_possible_start_codons, #return_array_of_one_letter_aminoacids, #return_cheerful_person, #return_chunked_display, #return_ubiquitin_sequence, #runmode?, #set_be_verbose, #set_runmode, #start_codon?, #stop_codons?, #strict_filter_away_invalid_aminoacids, #taxonomy_download_directory?, #three_to_one, #to_rna, #trailing_three_prime, #use_opn?, #verbose_truth, #was_or_were, #without_extname, #write_what_into

Methods included from BaseModule

#absolute_path, #default_file_read, #file_readlines

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens, #set_commandline_arguments

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods inherited from Base

#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #no_file_exists_at, #no_newlines, #project_yaml_directory?, #rds, #register_sigint, #return_pwd, #return_the_first_line_of_this_file, #word_wrap, #write_what_into

Methods included from InternalHashModule

#internal_hash?, #reset_the_internal_hash

Methods included from InferTheNamespaceModule

#infer_the_namespace, #namespace?

Constructor Details

#initialize(i = ARGV, run_already = true) ⇒ DisplayOpenReadingFrames

#

initialize

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb', line 14

def initialize(
    i           = ARGV,
    run_already = true
  )
  reset
  set_commandline_arguments(i)
  set_dna_sequence # ← This must come after set_commandline_arguments().
  # ======================================================================= #
  # === Handle blocks next:
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :show_three_frames
    # ===================================================================== #
    when :show_three_frames
      @display_reverse_frames = false
    end
  end
  run if run_already
end

Instance Method Details

#colourize_dna(i) ⇒ Object

#

colourize_dna

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 378

def colourize_dna(i)
  paleturquoise(i)
end

#colourize_this_aminoacid_sequence(i) ⇒ Object

#

colourize_this_aminoacid_sequence

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 175

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

#colourized_frame1 ⇒ Object

#

colourized_frame1

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 122

def colourized_frame1
  orange(' F1 ')
end

#colourized_frame2 ⇒ Object

#

colourized_frame2

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 129

def colourized_frame2
  orange(' F2 ')
end

#colourized_frame3 ⇒ Object

#

colourized_frame3

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 136

def colourized_frame3
  orange(' F3 ')
end

#colourized_reverse_frame1 ⇒ Object

#

colourized_reverse_frame1

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 143

def colourized_reverse_frame1
  orangered(' R1 ')
end

#colourized_reverse_frame2 ⇒ Object

#

colourized_reverse_frame2

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 150

def colourized_reverse_frame2
  orangered(' R2 ')
end

#colourized_reverse_frame3 ⇒ Object

#

colourized_reverse_frame3

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 157

def colourized_reverse_frame3
  orangered(' R3 ')
end

#determine_all_six_reading_frames(forward_sequence, reverse_dna_strand) ⇒ Object

#

determine_all_six_reading_frames

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb', line 62

def determine_all_six_reading_frames(
    forward_sequence, reverse_dna_strand
  )
  determine_frame1(forward_sequence)
  determine_frame2(forward_sequence)
  determine_frame3(forward_sequence)
  determine_reverse_frame1(reverse_dna_strand)
  determine_reverse_frame2(reverse_dna_strand)
  determine_reverse_frame3(reverse_dna_strand)
end

#determine_frame1(i = dna_sequence?) ) ⇒ Object

#

determine_frame1

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb', line 41

def determine_frame1(i = dna_sequence?)
  @hash[:frame1] = Bioroebe.to_aa(i)
end

#determine_frame2(i = dna_sequence?) ) ⇒ Object

#

determine_frame2

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb', line 48

def determine_frame2(i = dna_sequence?)
  @hash[:frame2] = Bioroebe.to_aa(i) { :frame2 }
end

#determine_frame3(i = dna_sequence?) ) ⇒ Object

#

determine_frame3

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb', line 55

def determine_frame3(i = dna_sequence?)
  @hash[:frame3] = Bioroebe.to_aa(i) { :frame3 }
end

#determine_reverse_frame1(i) ⇒ Object Also known as: determine_frame4

#

determine_reverse_frame1

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb', line 14

def determine_reverse_frame1(i)
  i = i.reverse.dup
  @hash[:reverse_frame1] = Bioroebe.to_aa(i)
end

#determine_reverse_frame2(i) ⇒ Object Also known as: determine_frame5

#

determine_reverse_frame2

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb', line 22

def determine_reverse_frame2(i)
  i = i.reverse.dup
  i[0,1] = ''
  @hash[:reverse_frame2] = Bioroebe.to_aa(i)
end

#determine_reverse_frame3(i) ⇒ Object Also known as: determine_frame6

#

determine_reverse_frame3

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb', line 31

def determine_reverse_frame3(i)
  i = i.reverse.dup
  i[0,1] = ''
  i[0,1] = ''
  @hash[:reverse_frame3] = Bioroebe.to_aa(i)
end

#display_modulo_ten_spacer(sequence_to_use = dna_sequence?, , optional_mode = :normal, use_this_padding = @left_padding) ⇒ Object

#

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.

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 393

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

#display_reverse_frame1(i = @hash[:reverse_frame1].reverse) ⇒ Object

#

display_reverse_frame1

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 276

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(i = @hash[:reverse_frame2].reverse) ⇒ Object

#

display_reverse_frame2

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 301

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(i = @hash[:reverse_frame3].reverse) ⇒ Object

#

display_reverse_frame3

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 325

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

#display_separator_in_the_middle(display_n_nucleotides = display_n_nucleotides? ) ⇒ Object Also known as: central_part

#

display_separator_in_the_middle (middle tag)

This method will display the separator in the middle.

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 201

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

#display_the_nucleotide_sequence_on_bottom(i = complementary_dna_strand(dna_sequence?)) ⇒ Object

#

display_the_nucleotide_sequence_on_bottom

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb', line 45

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

#display_the_nucleotide_sequence_on_top(i = dna_sequence?, , upper_range = display_n_nucleotides_per_line? ) ⇒ Object Also known as: show_top_sequence

#

display_the_nucleotide_sequence_on_top (top tag)

The second argument shows at which number this method will stop.

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 253

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

#display_the_three_regular_frames ⇒ Object

#

display_the_three_regular_frames

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 190

def display_the_three_regular_frames
  show_frame3
  show_frame2
  show_frame1
end

#dna_sequence? ⇒ Boolean

#

dna_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 31

def dna_sequence?
  @dna_sequence
end

#frame1? ⇒ Boolean

#

frame1?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 80

def frame1?
  @hash[:frame1]
end

#frame2? ⇒ Boolean

#

frame2?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 87

def frame2?
  @hash[:frame2]
end

#frame3? ⇒ Boolean

#

frame3?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 115

def frame3?
  @hash[:frame3]
end

#frame4? ⇒ Boolean

#

frame4?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 94

def frame4?
  @hash[:reverse_frame1]
end

#frame5? ⇒ Boolean

#

frame5?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 101

def frame5?
  @hash[:reverse_frame2]
end

#frame6? ⇒ Boolean

#

frame6?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 108

def frame6?
  @hash[:reverse_frame3]
end

#left_padding? ⇒ Boolean Also known as: padding_to_use?

#

left_padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 371

def left_padding?
  @left_padding
end

#menu(i = commandline_arguments_with_two_leading_hyphens) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb', line 14

def menu(
    i = commandline_arguments_with_two_leading_hyphens
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i
    # ===================================================================== #
    # === --codon-table=yeast
    #
    # This entry point can be used to designate a specific codon table.
    #
    # Usage example:
    #
    #   displayopenreadingframes ATGGGAGCGATCGAAATACCAGCACTACCATGAATTCTATATGGCACTACCATGAATTGA --codon-table=bacteria
    #   displayopenreadingframes ATGGGAGCGATCGAAATACCAGCACTACCATGAATTCTATATGGCACTACCATGAATTGA --codon-table=yeast_mitochondria
    #
    # ===================================================================== #
    when /^-?-?codon(-|_)?table=(.+)$/i
      _ = $2.to_s.dup.to_sym
      Bioroebe.set_use_this_codon_table(_)
    # ===================================================================== #
    # === --threshold=30
    # ===================================================================== #
    when /^-?-?threshold=(.+)$/i
      set_threshold($1.to_s.dup)
    # ===================================================================== #
    # === display_open_reading_frames ATGGGAGCGATCGAAATACCAGCACTACCATGAATTC --no-reverse-frames
    # ===================================================================== #
    when /^-?-?no(-|_)?reverse(-|_)?frames$/i
      @display_reverse_frames = false
    end
  end
end

#replace_this_input_with_modulo_ten(sequence_to_use = dna_sequence?, , i = '-' * n_nucleotides?, , optional_mode = :default) ⇒ Object

#

replace_this_input_with_modulo_ten

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 422

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

#report_how_many_ORFs_are_found ⇒ Object

#

report_how_many_ORFs_are_found

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb', line 61

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 ⇒ Object

#

report_the_start_codons_and_the_stop_codons_in_use

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb', line 91

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

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb', line 14

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

#return_n_ORFs_in_this_sequence(i) ⇒ Object

#

return_n_ORFs_in_this_sequence

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb', line 111

def return_n_ORFs_in_this_sequence(i)
  ::Bioroebe.return_n_ORFs_in_this_sequence(i)
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 38

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

#set_dna_sequence(i = commandline_arguments?.first) ⇒ Object

#

set_dna_sequence

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 14

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

#set_split_at_n_characters(i) ⇒ Object Also known as: set_threshold

#

set_split_at_n_characters

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 364

def set_split_at_n_characters(i)
  @split_at_n_characters = i.to_i
end

#show_frame1(i = frame1? ) ⇒ Object

#

show_frame1

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 240

def show_frame1(
    i = frame1?
  )
  e @left_padding+
    colourize_this_aminoacid_sequence(two_spaces_padding(i))+
    colourized_frame1
end

#show_frame2(i = frame2? ) ⇒ Object

#

show_frame2

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 229

def show_frame2(
    i = frame2?
  )
  e @left_padding+' '+
    colourize_this_aminoacid_sequence(two_spaces_padding(i, -1))+
    colourized_frame2
end

#show_frame3(i = frame3? ) ⇒ Object

#

show_frame3

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 218

def show_frame3(
    i = frame3?
  )
  e @left_padding+'  '+
    colourize_this_aminoacid_sequence(two_spaces_padding(i, -2))+
    colourized_frame3
end

#show_the_intro_for_this_class ⇒ Object

#

show_the_intro_for_this_class

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb', line 16

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

#split_at_n_characters? ⇒ Boolean Also known as: display_n_nucleotides_per_line?, display_n_nucleotides?, n_nucleotides_per_line?, n_nucleotides?, n_nucleotides, threshold_value?

#

split_at_n_characters?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 410

def split_at_n_characters?
  @split_at_n_characters
end

#two_spaces_padding(i, modify_the_padding_by_this = 0) ⇒ Object

#

two_spaces_padding

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 164

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

#two_spaces_padding_last(i, modify_the_padding_by_this = 0) ⇒ Object

#

two_spaces_padding_last

#


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# File 'lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb', line 349

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