Class: Bioroebe::CountAmountOfNucleotides

Inherits:
CommandlineApplication show all
Defined in:
lib/bioroebe/count/count_amount_of_nucleotides.rb

Overview

Bioroebe::CountAmountOfNucleotides

Constant Summary collapse

USE_THIS_START_CODON =
#

USE_THIS_START_CODON

#
'ATG'
DEFAULT_DNA_STRING_TO_USE =
#

DEFAULT_DNA_STRING_TO_USE

#
'ATCGAAAAAAATAAATAAAACAAATATATA'
FORMAT_STRING1 =
#

FORMAT_STRING1

#
'%-12s'
FORMAT_STRING2 =
#

FORMAT_STRING2

#
'%4s'

Constants inherited from CommandlineApplication

Bioroebe::CommandlineApplication::OLD_VERBOSE_VALUE

Constants included from ColoursForBase

Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Constants inherited from Base

Base::NAMESPACE

Class Method Summary collapse

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(this_dna_string = DEFAULT_DNA_STRING_TO_USE, run_already = true) ⇒ CountAmountOfNucleotides

#

intitialize

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 49

def initialize(
    this_dna_string = DEFAULT_DNA_STRING_TO_USE,
    run_already     = true
  )
  super()
  reset
  this_dna_string = parse_commandline_arguments(this_dna_string)
  set_dna_string(
    this_dna_string
  )
  # ======================================================================= #
  # === Handle blocks given to this method next:
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    when :display_short_form
      @display_short_form = true
    else
      if yielded.is_a? Hash
        # ================================================================= #
        # === :use_colours
        # ================================================================= #
        if yielded.has_key? :use_colours
          set_use_colours(yielded.delete(:use_colours))
        end
      end
    end
  end
  case run_already
  # ======================================================================= #
  # === :do_not_run_yet
  # ======================================================================= #
  when :do_not_run_yet
    run_already = false
  # ======================================================================= #
  # === :use_cliner
  # ======================================================================= #
  when :use_cliner
    @use_cliner = true
    run_already = true
  end
  run if run_already
end

Class Method Details

.show_composition(i) ⇒ Object

#

CountAmountOfNucleotides.show_composition

This class method will return a Hash with the proper A,T,C,G count.

Specific Usage Example:

CountAmountOfNucleotides.show_composition "ATATTTGCCCTATTTTTCC" # => {"a"=>3, "t"=>10, "g"=>1, "c"=>5}
#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 457

def self.show_composition(i)
  _ = CountAmountOfNucleotides.new(i, false)
  hash = {}
  hash['A'] = _.n_a # n Adenines
  hash['T'] = _.n_t # n Thymines
  hash['G'] = _.n_g # n Guanosines
  hash['C'] = _.n_c # n Cytosines
  return hash
end

Instance Method Details

#dna_string? ⇒ Boolean

#

dna_string?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 259

def dna_string?
  @dna_string
end

#menu(i) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 155

def menu(i)
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i # case tag
    # ===================================================================== #
    # === --short-form
    # ===================================================================== #
    when /^-?-?short(-|_)?form$/i,
         /^-?-?short$/
      @display_short_form = true
    end
  end
end

#n_a(i = @dna_string) ⇒ Object

#

n_a

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 231

def n_a(i = @dna_string)
  i.count('A')
end

#n_c(i = @dna_string) ⇒ Object

#

n_c

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 245

def n_c(i = @dna_string)
  i.count('C')
end

#n_g(i = @dna_string) ⇒ Object

#

n_g

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 238

def n_g(i = @dna_string)
  i.count('G')
end

#n_t(i = @dna_string) ⇒ Object

#

n_t

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 252

def n_t(i = @dna_string)
  i.count('T')
end

#parse_commandline_arguments(i) ⇒ Object

#

parse_commandline_arguments

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 135

def parse_commandline_arguments(i)
  if i.is_a? Array
    if i.any? {|entry| entry.start_with? '--' }
      # =================================================================== #
      # All entries leading with two '-' will be passed into menu()
      # and also be removed from the given input. We let code in
      # base.rb deal with this, though.
      # =================================================================== #
      menu(
        select_entries_starting_with_two_hyphens(i)
      )
      i.reject! {|entry| entry.start_with? '--' }
    end
  end
  i
end

#report_AT_content(n_percent = :calculate_anew) ⇒ Object

#

report_AT_content

This method is, for now, a dependent method - the method report_GC_content does the calculation.

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 208

def report_AT_content(n_percent = :calculate_anew)
  case n_percent
  when :calculate_anew
    n_percent = ((
                  @hash_percentages['A']+@hash_percentages['T']
                ) * 100.0) / @dna_string.size
  end
  erev 'The AT content (A+T) is: '+
        sfancy(n_percent.round(2).to_s)+rev+' %'
end

#report_everything(i = @dna_string) ⇒ Object

#

report_everything

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 333

def report_everything(
    i = @dna_string
  )
  if i.empty?
    erev '@dna_string is empty, this means that you have not yet assigned a '
    erev 'string. Please assign a DNA string to this class first.'
  else
    # ===================================================================== #
    # This else clause can output too much / too long strings.
    #
    # Since this can become quite spammy, we will report a truncated
    # version.
    # ===================================================================== #
    erev "Analyzing the DNA string `"+
      colourize_dna(
        remove_escape_sequences(
          return_truncated_dna_string(:default, false)
        ),
        use_colours?
      )+
      "#{rev}"+
      return_colourized_truncated_at_message+
      "`.#{N}#{N}"
    n_nucleotides = i.size.to_i
    erev "These #{simp(n_nucleotides.to_s)}#{rev} Nucleotides "\
         "were found:#{rev}#{N}#{N}"
    cliner if @use_cliner
    set_percentage_of(:adenine)
    e
    erev @l_padding+slateblue(@format_string1 % 'Adenines: ')+simp(
      (@format_string2 % n_a)
    )+@percentage
    set_percentage_of(:guanine)
    erev @l_padding+slateblue(@format_string1 % 'Guanines: ')+simp(
      (@format_string2 % n_g)
    )+@percentage
    set_percentage_of(:cytosine)
    erev @l_padding+slateblue(@format_string1 % 'Cytosines: ')+simp(
      (@format_string2 % n_c)
    )+@percentage
    set_percentage_of(:thymine)
    erev @l_padding+slateblue(@format_string1 % 'Thymine: ')+simp(
      (@format_string2 % n_t)
    )+@percentage+N+rev # Append extra newline.
    cliner if @use_cliner
    report_total_amount
    report_how_many_start_codons_exist
  end
end

#report_GC_content ⇒ Object Also known as: report_gc_content

#

report_GC_content

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 195

def report_GC_content
  n_percent = ((
    @hash_percentages['G']+@hash_percentages['C']
  ) * 100.0) / @dna_string.size
  erev "The GC content (G+C) is: #{sfancy(n_percent.round(2).to_s)}#{rev} %"
end

#report_how_many_nucleotides_we_have_found ⇒ Object

#

report_how_many_nucleotides_we_have_found

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 308

def report_how_many_nucleotides_we_have_found
  erev "#{N}In total "\
       "#{simportant(@dna_string.size.to_s)}#{rev} nucleotides were found."
end

#report_how_many_start_codons_exist ⇒ Object

#

report_how_many_start_codons_exist

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 316

def report_how_many_start_codons_exist
  n_start_codons = dna_string?.scan(/#{USE_THIS_START_CODON}/).size
  erev "In the given DNA string "\
       "#{simp(n_start_codons)}#{rev} start codons ("\
       "#{return_colourized_start_codon}#{rev}) were found.#{N}"
end

#report_the_amount_of_nucleotides_in_short_form_on_a_single_line ⇒ Object

#

report_the_amount_of_nucleotides_in_short_form_on_a_single_line

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 280

def report_the_amount_of_nucleotides_in_short_form_on_a_single_line
  # ======================================================================= #
  # Output will be:
  #
  #   A G C T
  #
  # ======================================================================= #
  e return_the_amount_of_nucleotides_in_short_form_on_a_single_line
end

#report_total_amount ⇒ Object

#

report_total_amount

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 222

def report_total_amount
  report_how_many_nucleotides_we_have_found
  report_AT_content
  report_GC_content
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 97

def reset
  super()
  # ======================================================================= #
  # === @format_string1
  # ======================================================================= #
  @format_string1 = FORMAT_STRING1
  # ======================================================================= #
  # === @format_string2
  # ======================================================================= #
  @format_string2 = FORMAT_STRING2
  # ======================================================================= #
  # === @use_cliner
  # ======================================================================= #
  @use_cliner = false
  # ======================================================================= #
  # === @display_short_form
  # ======================================================================= #
  @display_short_form = false # If this is true, we will only report the numbers.
  # ======================================================================= #
  # === @hash_percentages
  # ======================================================================= #
  @hash_percentages = {}
  # ======================================================================= #
  # === @l_padding
  #
  # l_padding means left_padding. We must make this more dynamic,
  # in that it must depend on the amount of nucleotides given.
  # ======================================================================= #
  @l_padding  = '  '
  # ======================================================================= #
  # === @dna_string
  # ======================================================================= #
  @dna_string = ''.dup
end

#return_colourized_start_codon ⇒ Object Also known as: colourized_start_codon

#

return_colourized_start_codon

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 273

def return_colourized_start_codon
  swarn(USE_THIS_START_CODON)
end

#return_colourized_truncated_at_message ⇒ Object

#

return_colourized_truncated_at_message

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 326

def return_colourized_truncated_at_message
  " [#{swarn('TRUNCATED at 80')}#{rev}]"
end

#return_the_amount_of_nucleotides_in_short_form_on_a_single_line ⇒ Object

#

return_the_amount_of_nucleotides_in_short_form_on_a_single_line

The order of nucleotides that is to be favoured here, is:

A C G T
#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 298

def return_the_amount_of_nucleotides_in_short_form_on_a_single_line
  n_a.to_s+' '+ # A
  n_c.to_s+' '+ # C
  n_g.to_s+' '+ # G
  n_t.to_s      # T
end

#return_truncated_dna_string(do_truncate = :default, add_the_truncated_at_notice = true) ⇒ Object

#

return_truncated_dna_string

We can toggle whether we truncate or whether we will not.

Since as of December 2020, the truncate-notification will only be shown if the input-sequence length exceeds the threshold value.

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 392

def return_truncated_dna_string(
    do_truncate                 = :default,
    add_the_truncated_at_notice = true
  )
  case do_truncate
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    do_truncate = Bioroebe.do_truncate?
  end
  dna_string = @dna_string
  if dna_string.size > 100
    _ = ''.dup
    _ << rev if add_the_truncated_at_notice
    _ << dna_string[0..79]
    _ << return_colourized_truncated_at_message if add_the_truncated_at_notice
    dna_string = _
  end if do_truncate
  return dna_string
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 439

def run
  if @display_short_form
    report_the_amount_of_nucleotides_in_short_form_on_a_single_line
  else
    report_everything
  end
end

#set_dna_string(i = DEFAULT_DNA_STRING_TO_USE) ⇒ Object

#

set_dna_string

This method also supports loading the content of a file - if the given input is a locally existing file, then the content of said file will be used.

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 421

def set_dna_string(
    i = DEFAULT_DNA_STRING_TO_USE
  )
  i = DEFAULT_DNA_STRING_TO_USE if i.nil?
  if File.exist? i.to_s
    i = File.read(i.to_s).strip.delete(N)
  end
  if i.is_a? Array
    i = i.join(' ').strip
  end
  i = i.to_s.dup if i.frozen?
  i.upcase! # Want to keep it upcased.
  @dna_string = i
end

#set_percentage_of(i) ⇒ Object

#

set_percentage_of

#


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 173

def set_percentage_of(i)
  case i
  when :adenine,
       :guanine,
       :cytosine,
       :thymine
    i = i.to_s[0,1].capitalize
  end
  n_times = @dna_string.count(i.to_s)
  @hash_percentages[i] = n_times
  n_times = n_times.to_f * 100
  total_size = @dna_string.size.to_f
  percentage = n_times / total_size
  percentage = '%.2f' % percentage
  percentage.prepend ' ' if percentage.size == 4 # Prepend ' '.
  @percentage = rev+' | '+percentage.to_s+' '+
                swarn('%')
end

#string? ⇒ Boolean Also known as: string

#

string?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/count/count_amount_of_nucleotides.rb', line 266

def string?
  @string
end