Class: Bioroebe::CalculateMeltingTemperatureForMoreThanThirteenNucleotides

Inherits:
Base
  • Object
show all
Defined in:
lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb

Overview

Bioroebe::CalculateMeltingTemperatureForMoreThanThirteenNucleotides

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
BASE_VALUE =
#

BASE_VALUE

#
100.5

Constants included from ColoursForBase

Bioroebe::ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Instance Method Summary collapse

Methods inherited from Base

#append_what_into, #can_base_pair?, #convert_global_env, #delete_file, #directory_to_the_codon_tables?, #file_readlines, #infer_the_namespace, #is_on_roebe?, #is_palindrome?, #main_encoding?, #mkdir, #move_file, #mv, #namespace?, #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 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?

Constructor Details

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

#

initialize

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 55

def initialize(
    i           = ARGV,
    run_already = true
  )
  reset
  set_nucleotide_sequence(i)
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :do_not_report_anything
    # ===================================================================== #
    when :do_not_report_anything
      @do_report = false 
    end
  end
  run if run_already
end

Instance Method Details

#calculate_Tm_value ⇒ Object

#

calculate_Tm_value

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 182

def calculate_Tm_value
  result = BASE_VALUE
  # ======================================================================= #
  # Next, we will calculate the middle part:
  #
  #   (1)  (41 * (yG+zC) / (wA+xT+yG+zC))
  # 
  # ======================================================================= #
  middle_value1 = (  41.0 * (n_G?+n_C?) / n_nucleotides_in_total? )
  # ======================================================================= #
  # And this is the second middle value:
  #
  #   (820/(wA+xT+yG+zC)) + 16.6 * log10([Na+])
  #
  # ======================================================================= #
  middle_value2 = ( 820.0 / n_nucleotides_in_total? )
  result += ( middle_value1 - middle_value2)
  # ======================================================================= #
  # And the last part is the log result of the concentration of sodium:
  # ======================================================================= #
  log_result = 16.6 * log10(concentration_of_sodium)
  result += log_result
  @tm_value = result.round(3)
end

#concentration_of_sodium ⇒ Object

#

concentration_of_sodium

This reflects [Na+], that is the concentration of sodium.

For now it is hardcoded towards 50.0. In the future this may have to be adjusted.

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 222

def concentration_of_sodium
  @sodium_concentration # This is mMol so 50m Mol is 0.050 Mol.
end

#count_frequencies_of_the_nucleotides ⇒ Object

#

count_frequencies_of_the_nucleotides

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 112

def count_frequencies_of_the_nucleotides
  _ = @nucleotide_sequence
  @n_A = _.count('A')
  @n_T = _.count('T')
  @n_G = _.count('G')
  @n_C = _.count('C') 
end

#log10(i) ⇒ Object

#

log10

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 240

def log10(i)
  Math.log10(i)
end

#n_A? ⇒ Boolean

#

n_A?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 147

def n_A?
  @n_A
end

#n_C? ⇒ Boolean

#

n_C?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 168

def n_C?
  @n_C
end

#n_G? ⇒ Boolean

#

n_G?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 161

def n_G?
  @n_G
end

#n_nucleotides_in_total? ⇒ Boolean

#

n_nucleotides_in_total?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 175

def n_nucleotides_in_total?
  input_sequence?.size
end

#n_T? ⇒ Boolean

#

n_T?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 154

def n_T?
  @n_T
end

#nucleotide_sequence? ⇒ Boolean Also known as: input_sequence?

#

nucleotide_sequence?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 123

def nucleotide_sequence?
  @nucleotide_sequence
end

#report_results_from_the_frequencies_and_the_size_of_the_sequence_at_hand ⇒ Object

#

report_results_from_the_frequencies_and_the_size_of_the_sequence_at_hand

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 130

def report_results_from_the_frequencies_and_the_size_of_the_sequence_at_hand
  if @do_report
    erev 'This nucleotide sequence has '+
         sfancy(@nucleotide_sequence.size.to_s)+
         rev+
         ' nucleotides. ('+orange(input_sequence?)+rev+')'
    erev "The nucleotide-frequencies are: "\
         "#{simp(n_A?.to_s+'xA')}#{rev}, "\
         "#{simp(n_T?.to_s+'xT')}#{rev}, "\
         "#{simp(n_G?.to_s+'xG')}#{rev}, "\
         "#{simp(n_C?.to_s+'xC')}#{rev}"
  end 
end

#report_the_tm_value ⇒ Object Also known as: report

#

report_the_tm_value (report tag)

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 247

def report_the_tm_value
  if @do_report
    erev 'The calculated Tm value (salt-adjusted Tm) '\
         'is: '+sfancy(@tm_value)+rev+'°C'
  end
end

#reset ⇒ Object

#

reset

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 77

def reset
  super()
  # ======================================================================= #
  # === @namespace
  # ======================================================================= #
  @namespace = NAMESPACE
  # ======================================================================= #
  # === @nucleotide_sequence
  # ======================================================================= #
  @nucleotide_sequence = nil
  # ======================================================================= #
  # === @do_report
  # ======================================================================= #
  @do_report = true
  # ======================================================================= #
  # Set the default sodium concentration next.
  # ======================================================================= #
  set_sodium_concentration(:default)
end

#run ⇒ Object

#

run

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 257

def run
  count_frequencies_of_the_nucleotides
  e if @do_report
  report_results_from_the_frequencies_and_the_size_of_the_sequence_at_hand
  calculate_Tm_value
  report_the_tm_value
  e if @do_report
end

#set_nucleotide_sequence(i) ⇒ Object

#

set_nucleotide_sequence

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 100

def set_nucleotide_sequence(i)
  if i.is_a? Array
    i = i.join.strip
  end
  i = i.dup if i.frozen?
  i.delete!(' ')
  @nucleotide_sequence = i
end

#set_sodium_concentration(i = :default) ⇒ Object

#

set_sodium_concentration

#

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 229

def set_sodium_concentration(i = :default)
  case i
  when :default
    i = 0.050
  end
  @sodium_concentration = i
end

#tm_value? ⇒ Boolean

#

tm_value?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb', line 210

def tm_value?
  @tm_value
end