Class: Bioroebe::ShowNucleotideSequence

Inherits:
Sequence show all
Includes:
ColoursForBase
Defined in:
lib/bioroebe/nucleotides/show_nucleotide_sequence.rb

Overview

Bioroebe::ShowNucleotideSequence

Constant Summary collapse

USE_THIS_COLOUR =
#

Bioroebe::ShowNucleotideSequence::USE_THIS_COLOUR

This colours is usually “steelblue”.

#
USE_THIS_COLOUR_FOR_DNA

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Sequence

Bioroebe::Sequence::REMOVE_INVALID_CHARACTERS, Bioroebe::Sequence::SHALL_WE_UPCASE

Instance Method Summary collapse

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_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Methods inherited from Sequence

[], #automatic_support_for_nucleotides, #description?, #index, #infer_type, #is_DNA?, #is_RNA?, #is_a_protein?, #is_a_protein_now, #map, #n_uracil?, #randomize, #remove_invalid_entries_from_the_dna_sequence, #remove_invalid_entries_from_the_dna_sequence!, #return_string_nucleotides_or_aminoacids, #sanitize_dataset, #sanitize_rna, #save_sequence_to_this_file, sequence_from_file, #set_description, #set_dna, #set_protein, #set_rna, #set_save_file, #set_sequence, #set_type, #shall_we_upcase?, #size?, #to_genbank, #to_regexp, #type?

Methods inherited from RawSequence

#+, #<<, #[]=, #calculate_levensthein_distance, #chars?, #complement, #composition?, #count, #delete, #delete!, #downcase, #each_char, #empty?, #find_substring_indices, #first_position=, #freeze, #gsub, #gsub!, #include?, #insert_at_this_position, #prepend, #remove_n_characters_from_the_left_side, #reverse, #reverse!, #reverse_complement, #scan, #set_raw_sequence, #shuffle, #size?, #split, #start_with?, #strip, #subseq, #to_s, #to_str, #tr!, #upcase!

Constructor Details

#initialize(this_sequence = 'ATCG', run_already = true) ⇒ ShowNucleotideSequence

#

initialize

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 36

def initialize(
    this_sequence = 'ATCG',
    run_already   = true
  )
  reset
  extend ::Bioroebe::CommandlineArguments # <- This comes here due to reset() otherwise be defind.
  if this_sequence.is_a? Array
    if this_sequence.any? {|entry| entry.start_with? '--' }
      set_commandline_arguments(
        select_commandline_arguments(this_sequence)
      )
      this_sequence.reject! {|inner_entry| inner_entry.start_with? '--' }
      menu(@commandline_arguments)
    end
  end
  set_this_sequence(
    this_sequence
  )
  case run_already
  # ======================================================================= #
  # === :do_not_run_yet
  # ======================================================================= #
  when :do_not_run_yet,
       :do_not_run
    run_already = false
  # ======================================================================= #
  # === :do_not_report_anything
  # ======================================================================= #
  when :do_not_report_anything
    do_not_report_anything
  end
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    # ===================================================================== #
    # === Handle Symbols next
    # ===================================================================== #
    if yielded.is_a? Symbol
      case yielded
      # =================================================================== #
      # === :colourize_start_codon
      # =================================================================== #
      when :colourize_start_codon
        do_colourize_the_start_codon
      end
    # ===================================================================== #
    # === Handle Hashes next
    # ===================================================================== #
    elsif yielded.is_a? Hash
      # =================================================================== #
      # === :colourize_this_subsequence
      #
      # This entry point can be used to supply any other subsequence
      # that the user wants to colourize.
      #
      # Usage example:
      #
      #   {{ colourize_this_subsequence: 'ATG' }}
      #
      # =================================================================== #
      if yielded.has_key? :colourize_this_subsequence
        search_for_this_substring(
          yielded[:colourize_this_subsequence]
        )
      end
    end
  end
  run if run_already
end

Instance Method Details

#clear_padding ⇒ Object

#

clear_padding

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 166

def clear_padding
  @padding_to_use = ''.dup
end

#colourize_dna_sequence(i = '') ⇒ Object Also known as: colour_for_nucleotides, colourize_rna_sequence

#

colourize_dna_sequence

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 481

def colourize_dna_sequence(i = '')
  ::Colours.send(USE_THIS_COLOUR, i.dup)
end

#display_with_prior_formatting(i = @sequence_for_display, &block) ⇒ Object

#

display_with_prior_formatting

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 499

def display_with_prior_formatting(
    i = @sequence_for_display, &block
  )
  do_show_the_ruler
  clear_padding
  format_this_nucleotide_sequence(i, &block)
  report(i) # Need to invoke the original method. Before May 2020 this was display().
end

#do_colourize_the_start_codon ⇒ Object

#

do_colourize_the_start_codon

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 528

def do_colourize_the_start_codon
  add_this_substring('ATG')
end

#do_not_report_anything ⇒ Object

#

do_not_report_anything

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 212

def do_not_report_anything
  @may_we_report = false
end

#do_show_the_ruler ⇒ Object

#

do_show_the_ruler

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 394

def do_show_the_ruler
  @show_ruler = true
end

#format_this_nucleotide_sequence(i = main_sequence_as_string? ) ⇒ Object Also known as: format, format_this_string

#

format_this_nucleotide_sequence

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 219

def format_this_nucleotide_sequence(
    i = main_sequence_as_string?
  )
  show_ruler               = @show_ruler
  padding_to_use           = @padding_to_use
  show_five_prime_leader   = @show_five_prime_leader
  show_three_prime_trailer = @show_three_prime_trailer
  # ======================================================================= #
  # The variable called result will contain our modified sequence that
  # is to be displayed on the commandline.
  # ======================================================================= #
  result                   = "#{padding_to_use}#{rev}".dup
  case i
  when nil
    i = string? if string?
  end
  i = i.dup if i.frozen?
  # ======================================================================= #
  # == Handle blocks given next
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :colourize_start_codon
    # ===================================================================== #
    when :colourize_start_codon
      do_colourize_the_start_codon
    # ===================================================================== #
    # === :show_ruler
    # ===================================================================== #
    when :show_ruler
      show_ruler = true
    # ===================================================================== #
    # === :without_colours
    # ===================================================================== #
    when :without_colours
      show_ruler = yielded
      do_show_the_ruler
    # ===================================================================== #
    # === :complementary_strand
    #
    # When we use this entry point, specifically, we will also
    # revert leader and trailer.
    # ===================================================================== #
    when :complementary_strand
      result << return_three_prime_leader
      i = complementary_strand(
        i.chars
      )
      show_five_prime_leader = false
      show_three_prime_trailer = :use_five_prime_trailer
    # ===================================================================== #
    # === :to_rna
    # ===================================================================== #
    when :to_rna,
         :rna
      i = to_rna(i)
    else
      if yielded.is_a? Hash
        # ================================================================= #
        # === :use_this_as_padding
        # ================================================================= #
        if yielded.has_key? :use_this_as_padding
          padding_to_use = yielded[:use_this_as_padding]
        end
        # ================================================================= #
        # === :colourize_this_subsequence
        # ================================================================= #
        if yielded.has_key? :colourize_this_subsequence
          set_search_for(yielded[:colourize_this_subsequence])
        end
        # ================================================================= #
        # === :ruler
        # ================================================================= #
        if yielded.has_key? :ruler
          _ = yielded.delete(:ruler)
          case _
          when :without_colours
            show_ruler = _
          end
        end
      end
    end
  end
  # ======================================================================= #
  # Consider showing the ruler next:
  # ======================================================================= #
  if show_ruler
    result_as_string = ::Bioroebe::Ruler.new(i, :default) {{ ruler: show_ruler }}.result_as_string?
    erev padding_to_use+
         result_as_string
  end
  if show_five_prime_leader
    result << return_five_prime_leader
  end
  # ======================================================================= #
  # We will next colourize the nucleotides that we determined should
  # be colourized, in particular ATG start codons.
  # ======================================================================= #
  if @use_colours and !@array_colourize_these_substrings.empty?
    # ===================================================================== #
    # In this case we will try to colourize substrings.
    # ===================================================================== #
    @array_colourize_these_substrings.each {|this_substring|
      if i and i.include?(this_substring)
        i.prepend(return_colour_for_the_dna_sequence)
        i.gsub!(
          /(#{this_substring})/,
          crimson('\1')+
          remove_trailing_escape_part(colour_for_nucleotides)
        )
      end
    }
  end
  # ======================================================================= #
  # Support for dashed-form display comes next:
  # ======================================================================= #
  if @show_in_dashed_form
    how_many_times = 3
    use_this_token_for_rejoining = '-'
    n_times = '.' * how_many_times.to_i
    use_this_regex = /#{n_times}/
    i = i.scan(use_this_regex).join(use_this_token_for_rejoining)
  end
  result << colourize_dna_sequence(i)+
            rev
  if show_three_prime_trailer
    case show_three_prime_trailer
    when :use_five_prime_trailer
      result << " - 5'"
    else
      result << " - 3'"
    end
  end
  set_sequence_for_display(
    result
  )
end

#menu(i = @commandline_arguments) ⇒ Object

#

menu (menu tag)

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 363

def menu(
    i = @commandline_arguments
  )
  if i and i.is_a?(Array)
    i.each {|entry| menu(entry) }
  else
    case i
    # ===================================================================== #
    # === --ruler
    #
    # This can be invoked by doing something like:
    #
    #   show_nucleotide_sequence ATGATTGCACGACACACATAAA --ruler
    #
    # ===================================================================== #
    when /^-?-?ruler$/i
      @show_ruler = true
    end
  end
end

#report(i = @sequence_for_display, &block) ⇒ Object Also known as: display

#

report (report tag)

This method will only do the reporting by default - not a new format-operation, unless a block has been given to it.

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 452

def report(
    i = @sequence_for_display,
    &block
  )
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :colourize_start_codon
    #
    # When a block is given then we actually have to re-format the main
    # string again.
    # ===================================================================== #
    when :colourize_start_codon
      do_colourize_the_start_codon
      format_this_string(i)
    # ===================================================================== #
    # === :complementary_strand
    # ===================================================================== #
    when :complementary_strand
      i = ::Bioroebe.complementary_strand(i)
    end
  end
  erev i
end

#report_this_sequence(i, &block) ⇒ Object

#

report_this_sequence

Usage example for this method:

@show_nucleotide_sequence.report_this_sequence(input) {{ padding_to_use: padding? }}
#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 406

def report_this_sequence(
    i, &block
  )
  if block_given?
    yielded = yield
    if yielded.is_a? Symbol
      case yielded
      # =================================================================== #
      # === :piped
      # =================================================================== #
      when :piped
        i.gsub!(/(...)/, "\\1|") # Add | at every third position.
      end
    elsif yielded.is_a? Hash
      # =================================================================== #
      # === :colourize_this_subsequence
      # =================================================================== #
      if yielded.has_key? :colourize_this_subsequence
        search_for_this_substring(
          yielded[:colourize_this_subsequence]
        )
      end
      # =================================================================== #
      # === :show_piped_output
      # =================================================================== #
      if yielded.has_key?(:show_piped_output) and (yielded[:show_piped_output] == true)
        i = i.gsub(/(...)/, "\\1|") # Add | at every third position.
      end
      # =================================================================== #
      # === :padding_to_use
      # =================================================================== #
      if yielded.has_key? :padding_to_use
        set_padding(yielded.delete(:padding_to_use))
      end
    end
  end
  format_this_nucleotide_sequence(i)
  report # Do not specify (i) here, as we will use the formatted-sequence for display instead.
end

#reset ⇒ Object

#

reset

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 111

def reset
  super()
  # ======================================================================= #
  # === @commandline_arguments
  # ======================================================================= #
  @commandline_arguments = []
  # ======================================================================= #
  # === @sequence_for_display
  # ======================================================================= #
  @sequence_for_display     = nil
  # ======================================================================= #
  # === @may_we_report
  # ======================================================================= #
  @may_we_report            = true
  # ======================================================================= #
  # === @use_colours
  # ======================================================================= #
  @use_colours              = true
  # ======================================================================= #
  # === @show_five_prime_leader
  # ======================================================================= #
  @show_five_prime_leader   = true
  # ======================================================================= #
  # === @show_three_prime_trailer
  # ======================================================================= #
  @show_three_prime_trailer = true
  # ======================================================================= #
  # === @padding_to_use
  #
  # How much padding to use when displaying something.
  # ======================================================================= #
  @padding_to_use = '       '.dup
  # ======================================================================= #
  # === @show_in_dashed_form
  #
  # The dashed form is e. g. "ATG-GGC-CGC". By default this is not
  # enable.
  # ======================================================================= #
  @show_in_dashed_form = false
  # ======================================================================= #
  # === @show_ruler
  #
  # The next variable determines whether a ruler will be displayed
  # on top of the nucleotide-sequence.
  # ======================================================================= #
  @show_ruler          = false
  # ======================================================================= #
  # === @array_colourize_these_substrings
  # ======================================================================= #
  @array_colourize_these_substrings = []
end

#return_colour_for_the_dna_sequence ⇒ Object

#

return_colour_for_the_dna_sequence

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 489

def return_colour_for_the_dna_sequence
  result = Colours.remove_trailing_code(
    ::Colours.send(USE_THIS_COLOUR)
  )
  return result
end

#return_five_prime_leader ⇒ Object

#

return_five_prime_leader

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 187

def return_five_prime_leader
  "5' - "
end

#return_three_prime_leader ⇒ Object

#

return_three_prime_leader

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 180

def return_three_prime_leader
  "3' - "
end

#run ⇒ Object

#

run

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 535

def run
  format_this_nucleotide_sequence
  report if @may_we_report
end

#search_for_this_substring(i) ⇒ Object Also known as: set_search_for, add_this_substring

#

search_for_this_substring

This method can be used to search for substrings, aka matches.

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 513

def search_for_this_substring(i)
  if i.is_a? Array
    i.each {|entry| search_for_this_substring(entry) }
  else
    unless @array_colourize_these_substrings.include? i
      @array_colourize_these_substrings << i
      @array_colourize_these_substrings.compact! # Added in 2021, to remove possible nil-values.
    end
  end
end

#sequence_for_display? ⇒ Boolean Also known as: formatted_sequence?, sequence_for_display

#

sequence_for_display?

This method will return the sequence that will be displayed on the commandline, for instance.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 204

def sequence_for_display?
  @sequence_for_display
end

#set_padding(i) ⇒ Object

#

set_padding

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 173

def set_padding(i)
  @padding_to_use = i
end

#set_sequence_for_display(i) ⇒ Object

#

set_sequence_for_display

#

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 194

def set_sequence_for_display(i)
  @sequence_for_display = i
end

#show_ruler? ⇒ Boolean

#

show_ruler?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/nucleotides/show_nucleotide_sequence.rb', line 387

def show_ruler?
  @show_ruler
end