Class: Bioroebe::ShowOrf

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/utility_scripts/showorf/showorf.rb

Overview

Bioroebe::ShowOrf

Constant Summary collapse

COLOURIZE_VERTICAL_TOKEN =
#

COLOURIZE_VERTICAL_TOKEN

#
true
LIMIT_AT_N_NUCLEOTIDES =
#

LIMIT_AT_N_NUCLEOTIDES

How many nucleotides we will display per given row.

This should not be a too high value, because it may otherwise overflow into the next line.

#
100
COLOURIZE_STOP_CODONS_IN_RED =
#

COLOURIZE_STOP_CODONS_IN_RED

If true then all ‘*’ will become red.

#
true

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, #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, show_these_frames = [:frame1], run_already = true) ⇒ ShowOrf

#

initialize

The first argument to this method should be the DNA nucleotide string whose ORF you wish to show.

The second argument to this method determines which frames to show.

The class assumes that the first input given is an Array, such as ARGV in particular.

#


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

def initialize(
    i                 = ARGV,     # The input should be an Array.
    show_these_frames = [:frame1],
    run_already       = true
  )
  reset
  # ======================================================================= #
  # First set up the default frames. This can be overruled lateron,
  # in particular upon the invocation of the method called
  # obtain_commandline_arguments_and_reject_double_separators.
  # ======================================================================= #
  set_show_these_frames(show_these_frames)
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    when :show_three_frames
      set_show_these_frames(:show_three_frames)
    else
      set_show_these_frames(yielded)
    end
  end
  # ======================================================================= #
  # Next, set the input sequence.
  # ======================================================================= #
  i = obtain_commandline_arguments_and_reject_double_separators(i)
  set_input_sequence(i)
  run if run_already
end

Instance Method Details

#colourize_stop_codons_in_red? ⇒ Boolean

#

colourize_stop_codons_in_red?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 405

def colourize_stop_codons_in_red?
  COLOURIZE_STOP_CODONS_IN_RED
end

#complement(i) ⇒ Object

#

complement

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 576

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

#default_padding(optional_remove_last_character_n_times = false) ⇒ Object Also known as: pad

#

default_padding (padding tag, pad tag)

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 385

def default_padding(
    optional_remove_last_character_n_times = false
  )
  result = '        '.dup
  if optional_remove_last_character_n_times
    optional_remove_last_character_n_times.abs.times { result.chop! }
  end
  return result
end

#frame_1? ⇒ Boolean Also known as: frame_1, frame1

#

frame_1?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 412

def frame_1?
  @frame_1
end

#frame_2? ⇒ Boolean Also known as: frame_2, frame2

#

frame_2?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 420

def frame_2?
  @frame_2
end

#frame_3? ⇒ Boolean Also known as: frame_3, frame3

#

frame_3?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 428

def frame_3?
  @frame_3
end

#hor_bar(i, how_many_times) ⇒ Object

#

hor_bar

This method is used to generate a horizontal bar.

The second argument tells it how many times to repeat the main token.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 558

def hor_bar(
    i,
    how_many_times
  )
  use_this_token = '-'
  # ======================================================================= #
  # Next, return the assembly.
  # ======================================================================= #
  token_pad+
  use_this_token+
  use_this_token+
  use_this_token+
  (i * how_many_times)
end

#inner_strip(i) ⇒ Object

#

inner_strip

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 252

def inner_strip(i)
  i.delete(' ')
end

#input_sequence? ⇒ Boolean Also known as: input?

#

input_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 272

def input_sequence?
  @input_sequence
end

#max_allowed_size_per_line ⇒ Object

#

max_allowed_size_per_line

This method will return a number, which states how many characters are allowed in the main header, above frame 1.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 450

def max_allowed_size_per_line
  _ = input?
  n_nucleotides = _.size + 2 + _.size.to_s.size
  return n_nucleotides
end

#menu(i = commandline_arguments? ) ⇒ Object

#

menu (menu tag)

By default, the input to this menu will be solely commandline arguments that have ‘–’ as part of their name.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 673

def menu(
    i = commandline_arguments?
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === showorf CACAGCAGCAGGCCCTCGGTCGTCGCTCCACATCAGCCGTCACATAGAGCTGATAG --all
    # ===================================================================== #
    when /^-?-?all$/
      set_show_these_frames(:all_frames)
    # ===================================================================== #
    # === showorf CACAGCAGCAGGCCCGTCACATAGAGCTGATAG --frame3
    # ===================================================================== #
    when /^-?-?frame3$/,
         /^-?-?show-?only-?frame-?3$/,
         /^-?-?f3$/
      set_show_these_frames(:f3)
    # ===================================================================== #
    # === showorf --frame2
    # ===================================================================== #
    when /^-?-?frame2$/,
         /^-?-?show-?only-?frame-?2$/,
         /^-?-?f2$/
      set_show_these_frames(:f2)
    # ===================================================================== #
    # === showorf --frames_1_2_3
    # ===================================================================== #
    when /^-?-?frames_?1_?2_?3/,
         /^-?-?show-?frame-?1-?2-?3/
      set_show_these_frames(:f1_and_f2_and_f3)
    # ===================================================================== #
    # === showorf --frame1-and-2
    # ===================================================================== #
    when /^-?-?frame-?1(_|-)?and(_|-)?2/
      set_show_these_frames(:f1_and_f2)
    # ===================================================================== #
    # === showorf --frame1
    # ===================================================================== #
    when /^-?-?frame1$/,
         /-?-?show-?only-?frame-?1/
      set_show_these_frames(:f1)
    # ===================================================================== #
    # === showorf --help
    # ===================================================================== #
    when /help/
      show_help
      exit
    end
  end
end

#n_nucleotides? ⇒ Boolean

#

n_nucleotides?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 398

def n_nucleotides?
  input?.size
end

#obtain_commandline_arguments_and_reject_double_separators(i) ⇒ Object

#

obtain_commandline_arguments_and_reject_double_separators

Presently, we only work on Arrays as input.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 238

def obtain_commandline_arguments_and_reject_double_separators(i)
  _ = i
  if i.is_a? Array
    if _.any? {|entry| entry.include? '--' }
      @commandline_arguments = _.select {|line| line.include? '--'}
      _.reject! {|line| line.include? '--'}
    end
  end
  return _
end

#orange_f1 ⇒ Object Also known as: f1

#

orange_f1

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 582

def orange_f1
  orange('  F1  ')+rev
end

#orange_f2 ⇒ Object Also known as: f2

#

orange_f2

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 589

def orange_f2
  orange('  F2  ')+rev
end

#orange_f3 ⇒ Object Also known as: f3

#

orange_f3

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 596

def orange_f3
  orange('  F3  ')+rev
end

#r1 ⇒ Object

#

r1

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 603

def r1
  orangered('  R1  ')+rev
end

#r2 ⇒ Object

#

r2

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 610

def r2
  orangered('  R2  ')+rev
end

#r3 ⇒ Object

#

r3

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 617

def r3
  orangered('  R3  ')+rev
end

#remove_newlines(i) ⇒ Object

#

remove_newlines

This method will simply remove all newlines.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 281

def remove_newlines(i)
  if i.is_a? Array
    i.flatten.map {|entry| remove_newlines(entry)}
  else
    i.delete(N)
  end
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 90

def reset
  super()
  infer_the_namespace
  # ======================================================================= #
  # === @show_these_frames
  #
  # Specify which frames are to be shown.
  #
  # By default, we will show all 3 forward and all 3 reverse frames.
  #
  # This can change on the commandline. For example,
  # showorf ATGCGC --only-frame-1 would keep only :frame1
  # in this array.  
  # ======================================================================= #
  @show_these_frames = [
    :frame1,
    :frame2,
    :frame3,
    :reverse_frame1,
    :reverse_frame2,
    :reverse_frame3,
  ]
end

#return_horizontal_bar(i = input?) ) ⇒ Object

#

return_horizontal_bar

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 539

def return_horizontal_bar(i = input?)
  _ = return_spacer * i.size
  # ======================================================================= #
  # Next, at every 10th position, replace.
  # ======================================================================= #
  _.gsub!(/----------/, '---------'+return_vertical_token)
  if _.size > LIMIT_AT_N_NUCLEOTIDES
    _ = _[0, LIMIT_AT_N_NUCLEOTIDES]
  end
  return _
end

#return_numbers_based_on_this_input(i) ⇒ Object

#

return_numbers_based_on_this_input

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 355

def return_numbers_based_on_this_input(i)
  _ = ''.dup
  case i.size
  when 11..20
    _ << '10'+pad
  when 21..29
    _ << '10'+pad+'20'+pad
  when 30..39
    _ << '10'+pad+'20'+pad+'30'+pad
  when 40..49
    _ << '10'+pad+'20'+pad+'30'+pad+'40'+pad
  when 50..59
    _ << '10'+pad+'20'+pad+'30'+pad+'40'+pad+'50'+pad
  when 60..69
    _ << '10'+pad+'20'+pad+'30'+pad+'40'+pad+'50'+pad+'60'+pad
  when 70..79
    _ << '10'+pad+'20'+pad+'30'+pad+'40'+pad+'50'+pad+'60'+pad+'70'+pad
  when 80..89
    _ << '10'+pad+'20'+pad+'30'+pad+'40'+pad+'50'+pad+'60'+pad+'70'+pad+'80'+pad
  when 90..99
    _ << '10'+pad+'20'+pad+'30'+pad+'40'+pad+'50'+pad+'60'+pad+'70'+pad+'80'+pad+'90'+pad
  else
    _ << '10'+pad+'20'+pad+'30'+pad+'40'+pad+'50'+pad+'60'+pad+'70'+pad+'80'+pad+'90'+pad(-1)+'100'+pad
  end
  return _ # Return it here.
end

#return_properly_formated_spacer_tokens(i) ⇒ Object

#

return_properly_formated_spacer_tokens

Input how many ‘-’ tokens you need to have for this line.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 531

def return_properly_formated_spacer_tokens(i)
  _ = return_spacer(i)
  _.gsub(/----------/, '---------'+return_vertical_token)
end

#return_spacer(n_spacer_tokens = 100) ⇒ Object

#

return_spacer

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 334

def return_spacer(n_spacer_tokens = 100)
  '-' * n_spacer_tokens.abs
end

#return_vertical_token ⇒ Object

#

return_vertical_token

If we want to return a colourized ‘|’ token.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 438

def return_vertical_token
  _ = '|'
  _ = palegreen(_)+rev if COLOURIZE_VERTICAL_TOKEN
  return _
end

#reverse_complement(i) ⇒ Object

#

reverse_complement

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 348

def reverse_complement(i)
  i = complement(i.reverse)
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 729

def run
  menu
  _ = input?.dup # Keep a pointer to the input given to us.
  n_nucleotides = _.size.to_s
  # ======================================================================= #
  # Chop the main string up into chunks of 100 each.
  # ======================================================================= #
  chopped_input = _.scan(/.{1,100}/m)
  converted_sequence_for_frame_1 = to_frame1(_)
  converted_sequence_for_frame_2 = to_frame2(_)
  converted_sequence_for_frame_3 = to_frame3(_)
  converted_sequence_for_reverse_frame_1 = to_reverse_frame1(_)
  converted_sequence_for_reverse_frame_2 = to_reverse_frame2(_)
  converted_sequence_for_reverse_frame_3 = to_reverse_frame3(_)
  e
  e "#{rev}Translation of requested code (5' #{steelblue('→')} #{rev}3') "\
    "for #{simp(n_nucleotides)}#{rev} nucleotides.#{N}"
  e
  # ======================================================================= #
  # Next, we build up the 3 different frames. In order to do so,
  # we will first insert two ' ' after every position.
  # ======================================================================= #
  converted_sequence_for_frame_1 = converted_sequence_for_frame_1.chars.map {|entry|
    entry+'  '
  }.join
  converted_sequence_for_frame_2 = ' '+converted_sequence_for_frame_2.chars.map {|entry|
    entry+'  '
  }.join
  converted_sequence_for_frame_3 = '  '+converted_sequence_for_frame_3.chars.map {|entry|
    entry+'  '
  }.join
  converted_sequence_for_reverse_frame_1 = converted_sequence_for_reverse_frame_1.chars.map {|entry|
    entry+'  '
  }.join
  converted_sequence_for_reverse_frame_2 = ' '+converted_sequence_for_reverse_frame_2.chars.map {|entry|
    entry+'  '
  }.join
  converted_sequence_for_reverse_frame_3 = '  '+converted_sequence_for_reverse_frame_3.chars.map {|entry|
    entry+'  '
  }.join
  # ======================================================================= #
  # We will chop them up into runs of 100, but only display
  # for how many we get. The seagreen bar is on the very top,
  # the "10    20" and so on.
  # ======================================================================= #
  e '                    '+
    seagreen(
      return_numbers_based_on_this_input(_)
    )+
    rev
  # ======================================================================= #
  # === Get rid of newlines
  # ======================================================================= #
  if chopped_input.any? {|entry| entry.include? N }
    chopped_input = remove_newlines(chopped_input)
  end
  chopped_input = strip(chopped_input)
  chopped_input.each_with_index {|aminoacids_in_this_line, index|

    left_nucleotide_position = ((index * 100)+1).to_s.rjust(3)
    right_position = ((100 * index)+aminoacids_in_this_line.size).to_s

    # ===================================================================== #
    # Return the properly formated spacer tokens next. We need to find
    # out how many tokens we have to display.
    # ===================================================================== #
    display_n_tokens = (right_position.to_i+1 - left_nucleotide_position.strip.to_i)

    # ===================================================================== #
    # Display the first frame next, then the other two frames.
    # ===================================================================== #
    set_frame_1(
      converted_sequence_for_frame_1[(100 * index)..((100 * index)+100-1)]
    ) if show_frame_1?

    set_frame_2(
      converted_sequence_for_frame_2[(100 * index)..((100 * index)+100-1)]
    ) if show_frame_2?

    set_frame_3(
      converted_sequence_for_frame_3[(100 * index)..((100 * index)+100-1)]
    ) if show_frame_3?
    # ===================================================================== #
    # Next add the '----|' separators.
    # ===================================================================== #
    e "           #{return_properly_formated_spacer_tokens(display_n_tokens)}"
    # ===================================================================== #
    # === Next show the main nucleotide sequence
    # ===================================================================== #
    e '      '+
      mediumspringgreen(left_nucleotide_position)+rev+
      '  '+
      mediumseagreen(aminoacids_in_this_line.upcase)+rev+'  '+
      mediumspringgreen( # <- This here is the end-part that is colourized.
        ((100 * index)+aminoacids_in_this_line.size).to_s
      )
    # ===================================================================== #
    # The number should be reset after a '*' character.
    # ===================================================================== #

    # ===================================================================== #
    # === Handle Frame1 next
    # ===================================================================== #
    if show_frame_1?
      show_this_frame(frame_1, :frame1)
    end

    # ===================================================================== #
    # === Handle Frame2
    # ===================================================================== #
    if show_frame_2?
      show_this_frame(frame_2, :frame2)
    end

    # ===================================================================== #
    # === Handle Frame3
    # ===================================================================== #
    if show_frame_3?
      show_this_frame(frame_3, :frame3)
    end

    # ===================================================================== #
    # Next, consider showing the reverse frames.
    # ===================================================================== #
    if show_reverse_frame_1?
      e r1+'     '+converted_sequence_for_reverse_frame_1
    end

    if show_reverse_frame_2?
      e r2+'     '+converted_sequence_for_reverse_frame_2
    end

    if show_reverse_frame_3?
      e r3+'     '+converted_sequence_for_reverse_frame_3
    end

    e
  }
end

#set_frame_1(i) ⇒ Object

#

set_frame_1

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 303

def set_frame_1(i)
  i = i.to_s
  @frame_1 = i
end

#set_frame_2(i) ⇒ Object

#

set_frame_2

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 311

def set_frame_2(i)
  i = i.to_s
  @frame_2 = i
end

#set_frame_3(i) ⇒ Object

#

set_frame_3

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 319

def set_frame_3(i)
  i = i.to_s
  @frame_3 = i
end

#set_input_sequence(i) ⇒ Object

#

set_input_sequence

Set the DNA sequence here.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 261

def set_input_sequence(i)
  i = i.join if i.is_a? Array
  i = remove_newlines(i)
  i = strip(i) # Get rid of trailing thingies.
  i = inner_strip(i)
  @input_sequence = i
end

#set_show_these_frames(i) ⇒ Object

#

set_show_these_frames

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 117

def set_show_these_frames(i)
  case i # case tag
  # ======================================================================= #
  # === frame1
  # ======================================================================= #
  when :frame1,
       :f1
    @show_these_frames = [:frame1]
  # ======================================================================= #
  # === frame2
  # ======================================================================= #
  when :frame2,
       :f2
    @show_these_frames = [:frame2]
  # ======================================================================= #
  # === frame3
  # ======================================================================= #
  when :frame3,
       :f3
    @show_these_frames = [:frame3]
  # ======================================================================= #
  # === frame1_frame
  # ======================================================================= #
  when :frame1_frame2,
       :f1_and_f2
    @show_these_frames = [:frame1, :frame2]
  # ======================================================================= #
  # === f1_and_f2_and_f3
  # ======================================================================= #
  when :f1_and_f2_and_f3
    @show_these_frames = [:frame1, :frame2, :frame3]
  # ======================================================================= #
  # === all_frames                                                (all tag)
  #
  # Use this when you wish to show all 6 reading frames.
  # ======================================================================= #
  when :all_frames,
       :show_three_frames,
       :frame1_frame2_frame3,
       :frame1_frame2_frame2_reverse1_reverse2_reverse3
    @show_these_frames = [
      :frame1,
      :frame2,
      :frame3,
      :reverse_frame1,
      :reverse_frame2,
      :reverse_frame3
    ]
  end
end

#show_frame_1? ⇒ Boolean

#

show_frame_1?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 194

def show_frame_1?
  @show_these_frames.include? :frame1
end

#show_frame_2? ⇒ Boolean

#

show_frame_2?

#

Returns:

  • (Boolean) 


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

def show_frame_2?
  @show_these_frames.include? :frame2
end

#show_frame_3? ⇒ Boolean

#

show_frame_3?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 208

def show_frame_3?
  @show_these_frames.include? :frame3
end

#show_help ⇒ Object

#

show_help (help tag)

Invocation example:

showorf --help
#


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

def show_help
  e
  opnerev 'This class is capable of showing the ORF (open '\
             'reading frame) from the'
  opnerev 'given input string (which is assumed to be a '\
             'nucleotide sequence).'
  e
  opnerev 'By default, this class will show all 3 reading frames, but'
  opnerev 'you can also selectively show only one frame. Examples:'
  e
  opnerev '  --frame1 # show reading frame1 (forward frame 1)'
  opnerev '  --frame2 # show reading frame1 (forward frame 2)'
  opnerev '  --frame3 # show reading frame1 (forward frame 3)'
  e
end

#show_reverse_frame_1? ⇒ Boolean

#

show_reverse_frame_1?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 215

def show_reverse_frame_1?
  @show_these_frames.include? :reverse_frame1
end

#show_reverse_frame_2? ⇒ Boolean

#

show_reverse_frame_2?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 222

def show_reverse_frame_2?
  @show_these_frames.include? :reverse_frame2
end

#show_reverse_frame_3? ⇒ Boolean

#

show_reverse_frame_3?

#

Returns:

  • (Boolean) 


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

def show_reverse_frame_3?
  @show_these_frames.include? :reverse_frame3
end

#show_this_frame(i = frame_1, which_frame = :frame1) ⇒ Object

#

show_this_frame

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 624

def show_this_frame(
    i           = frame_1,
    which_frame = :frame1
  )
  _ = max_allowed_size_per_line
  n_aminoacids = i.delete(' ').chars.size.to_s
  right_padding = '  '.dup
  case which_frame
  when :frame1
    which_frame = orange_f1
    right_padding << '  '
  when :frame2
    which_frame = orange_f2
    right_padding << ' '
  when :frame3
    which_frame = orange_f3
  end
  leading_part = which_frame+(' ' * 3)+'  '+i
  # ======================================================================= #
  # === Colourize stop codons in the colour red
  # ======================================================================= #
  if colourize_stop_codons_in_red? and use_colours?
    leading_part.gsub!(/(\*)/, swarn('\\1')+rev)
  end
  leading_part << right_padding
  # ======================================================================= #
  # We may have to modify the variable n_aminoacids if there is a stop
  # codon.
  # ======================================================================= #
  if i.include? '*'
    n_aminoacids = i[(i.rindex('*')+1) .. i.size].delete(' ').size.to_s.
                   rjust(i.size.to_s.size)
  end
  # ======================================================================= #
  # Next also append how many aminoacids are part of this squence:
  # ======================================================================= #
  string = leading_part+
           darkolivegreen(
             n_aminoacids.to_s+' aminoacids'
           )+rev
  e string
end

#strip(i) ⇒ Object

#

strip

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 292

def strip(i)
  if i.is_a? Array
    i.map {|entry| strip(entry) }
  else
    i.strip
  end
end

#to_frame1(i) ⇒ Object

#

to_frame1

Frame1 requires no change, so we can simply pass it into the method Bioroebe.translate_dna_into_aminoacid().

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 462

def to_frame1(i)
  return ::Bioroebe.translate_dna_into_aminoacid(
    i
  ) # We need the module-method here.
end

#to_frame2(i) ⇒ Object

#

to_frame2

Frame2 requires a change, hence the second line in the method body.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 473

def to_frame2(i)
  i = i.dup
  i[0,1] = '' # Chop off the first character.
  return ::Bioroebe.translate_dna_into_aminoacid(
    i
  )
end

#to_frame3(i) ⇒ Object

#

to_frame3

Frame3 requires a change.

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 486

def to_frame3(i)
  i = i.dup
  i[0,1] = '' # Chop off the first character.
  i[0,1] = '' # And again.
  return ::Bioroebe.translate_dna_into_aminoacid(
    i
  )
end

#to_reverse_frame1(i) ⇒ Object

#

to_reverse_frame1

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 506

def to_reverse_frame1(i)
  i = reverse_complement(i).dup
  i[0,1] = ''
  return ::Bioroebe.translate_dna_into_aminoacid(
    i
  )
end

#to_reverse_frame2(i) ⇒ Object

#

to_reverse_frame2

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 517

def to_reverse_frame2(i)
  i = reverse_complement(i).dup
  i[0,1] = ''
  i[0,1] = ''
  return ::Bioroebe.translate_dna_into_aminoacid(
    i
  )
end

#to_reverse_frame3(i) ⇒ Object

#

to_reverse_frame3

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 498

def to_reverse_frame3(i)
  i = reverse_complement(i).dup
  return ::Bioroebe.translate_dna_into_aminoacid(i)
end

#token_pad ⇒ Object

#

token_pad

#


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 341

def token_pad
  '--------' # Horizontal padding.
end

#total_length? ⇒ Boolean Also known as: total_size?

#

total_length?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/utility_scripts/showorf/showorf.rb', line 327

def total_length?
  input?.size
end