Module: Diadem::Cubic

Defined in:
lib/diadem/cubic.rb,
lib/diadem/cubic/commandline.rb

Defined Under Namespace

Modules: Commandline Classes: Enrichment, Isotope, Peptide

Constant Summary collapse

FILE_EXT = 
'.cubic.csv'

Class Method Summary collapse

Class Method Details

.is_filename?(arg) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/diadem/cubic.rb', line 86

def is_filename?(arg)
  arg.include?('.') 
end

.run(argv) ⇒ Object

returns the filename of the output if given a filename, or nil



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# File 'lib/diadem/cubic.rb', line 15

def run(argv)
  (argv, opt) = Diadem::Cubic::Commandline.parse(argv)
  opt.isotope = Diadem::Cubic::Isotope.new( opt.element, opt.mass_number )
  opt.delim = ","
  (out, aaseqs) = 
    if is_filename?(argv.first)
      arg = argv.first
      base = arg.chomp(File.extname(arg))
      [File.open(base + FILE_EXT, 'w'), CSV.read(arg).map(&:first)]
    else
      [$stdout, argv]
    end
  calc = Diadem::Calculator.new( *opt.isotope.values )

  if opt.header
    cats = %w(sequence mods formula mass n)
    isotopomers = *opt.num_isotopomers.times.map {|n| "M#{n}" }
    cats.push(*isotopomers)
    isotopomers.each do |label|
      lowest_coeff = opt.return_zero_coeff ? 0 : 1
      (opt.degree).downto(lowest_coeff) do |coeff|
        cats << [label, "coeff", coeff].join("_")
      end
    end
    out.puts cats.join(opt.delim)
  end

  aaseqs.compact!  # ignore blank lines
  aaseqs.uniq! if opt.remove_duplicates

  aaseqs.each do |aaseq|
    # we cannot ensure the base 0% has been included in the range, so
    # calculate it separately
    mods = []
    if opt.carbamidomethyl
      mods << Diadem::Calculator::Modification::CARBAMIDOMETHYL
    end
    if opt.oxidized_met
      mods << Diadem::Calculator::Modification::OXIDIZED_METHIONINE
    end
    if opt.pyroglutamate_from_glutamine
      mods << Diadem::Calculator::Modification::PYROGLUTAMATE_Q
    end

    (distributions, info) = calc.calculate_isotope_distributions(aaseq, opt.range.dup, mods: mods)
    polynomials = Diadem::Calculator.distributions_to_polynomials(opt.range.to_a, distributions, opt.num_isotopomers, opt.degree)

    zero_pct_dist = 
      if opt.range.first == 0.0
        distributions.first
      else
        (dists, info) = calc.calculate_isotope_distributions(aaseq, [0.0])
        zero_pct_dist = dists.first
      end

    modinfo = info.mods.map {|match, mod| "#{match}:#{mod.sign}#{mod.diff_formula}" }.join(' ')
    line = [aaseq, modinfo, info.formula, info.formula.mass.round(6), info.penetration]
    line.push *zero_pct_dist.intensities[0,opt.num_isotopomers].map {|v| v.round(6) }
    polynomials.each do |coeffs|
      rev_coeffs = coeffs.reverse
      rev_coeffs.pop unless opt.return_zero_coeff
      line.push *rev_coeffs
    end
    out.puts line.join(opt.delim)
  end
  if out.respond_to?(:path)
    out.close
    out.path
  end
end