diadem 0.0.2

checksums.yaml

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+---
+SHA1:
+  metadata.gz: e43300c479c268f5db7b16b84b3b807e449757ad
+  data.tar.gz: 3a930a150873d4b004cb0d677992c98c0e4c2c4e
+SHA512:
+  metadata.gz: 17de7bc9c431c7917fb3136fc01ef8aace5a4ae383f615971ec3be8525d85dd722775ec05e6b259d2f869648a52b66c3eda14d9b2ee0cfe2d8db6d1a7c2609af
+  data.tar.gz: ffd5b0ace3d2cbb6f761d5e329afe3c961e96ca8e3311d4e68000b79af23e8423b9105bb2931f9d4ed1019b17a4e2c5eec120e1526426e194f0c10a2ef40cdc9

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+/gold_standards
+/*.png

data/Gemfile

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+source 'https://rubygems.org'
+
+gem 'mspire', :github => 'princelab/mspire', :branch => 'master'
+
+# Specify your gem's dependencies in diadem.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Brigham Young University
+Authored by: John T. Prince with guidance from John C. Price
+
+Please contact the authors if you would like to make arrangements to obtain
+the software under a different license.
+
+This program is free software: you can redistribute it and/or modify it under
+the terms of the GNU General Public License as published by the Free Software
+Foundation, either version 3 of the License, or (at your option) any later
+version.
+
+This program is distributed in the hope that it will be useful, but WITHOUT
+ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+details.
+
+You should have received a copy of the GNU General Public License along with
+this program.  If not, see <http://www.gnu.org/licenses/>.

data/README.md

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+# Diadem
+
+Tools for performing mass isotopomer distribution analysis (MIDA).  Basically,
+this is dynamic isotope analysis useful for mass spectrometry experiments
+involving protein turnover.
+
+## Installation
+
+NOTE: requires ruby >= 2.0
+
+Until the Mercury7 algorithm is implemented you will need the fftw3 gem
+installed.  It depends on the fftw3 library.  On Ubuntu/Debian, it's as easy
+as this:
+
+    sudo apt-get install libfftw3-dev
+
+Then
+
+    sudo gem install diadem
+
+## Examples
+
+Run diadem-cubic.rb from the commandline with no args to get help:
+
+    diadem-cubic.rb
+
+## LICENSE
+
+GNU Public License version 3 (see LICENSE.txt).  Please contact the authors for 
+consideration of releasing the software under different terms.
+
+## Acronym 
+
+Diadem stands for Dynamic Isotope Analysis DEMystified or maybe Dynamic Isotope
+Analysis DEMarcated.

data/Rakefile

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+require "bundler/gem_tasks"
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "rubabel #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/bin/diadem-cubic.rb

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+#!/usr/bin/env ruby
+
+require 'diadem/cubic'
+
+Diadem::Cubic.run(ARGV)

data/diadem.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'diadem/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "diadem"
+  spec.version       = Diadem::VERSION
+  spec.authors       = ["John Prince"]
+  spec.email         = ["jtprince@gmail.com"]
+  spec.description   = %q{Dynamic isotope analysis for mass spectrometry isotope experiments.  Calculates and visualizes varying isotope ratios and allows the user fine control over incorporation rates.}
+  spec.summary       = %q{Dynamic isotope analysis for mass spectrometry isotope experiments}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  [
+    ["mspire", "~> 0.10.0"],
+    ["fftw3", "~> 0.3"],
+  ].each do |args|
+    spec.add_dependency(*args)
+  end
+
+  [
+    ["bundler", "~> 1.3"],
+    ["rake"],
+    ["rspec", "~> 2.13.0"], 
+    ["rdoc", "~> 3.12"], 
+    ["simplecov"],
+    ["gnuplot", "~> 2.6.2"],
+  ].each do |args|
+    spec.add_development_dependency(*args)
+  end
+
+end

data/lib/diadem/calculator.rb

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+require 'matrix'
+
+require "diadem/version"
+require "diadem/enrichment"
+require "diadem/distribution"
+require 'mspire/molecular_formula'
+require 'mspire/isotope/distribution'
+
+module Diadem
+  class Calculator
+    # a match (a regex or a String of length 1) that indicates which amino
+    # acid should be modified, diff_formula is an Mspire::MolecularFormula
+    # object, gain  is whether the molecular formula is added or subtracted
+    # (boolean, default true).  static is boolean, default true.  match_block
+    # by default will merely return the thing being matched (which is good
+    # behavior for static mods)
+    Modification = Struct.new(:match, :diff_formula, :gain, :static, :match_block) do
+      def initialize(*args, &_match_block)
+        (_char, _formula, _gain, _static) = args
+        _gain.nil? && ( _gain=true )
+        _static.nil? && ( _static=true )
+        _match_block.nil? && (_match_block=Diadem::Calculator::Modification::STATIC_MATCH_BLOCK)
+        super(_char, _formula, _gain, _static, _match_block)
+      end
+
+      # the arithmetic sign as a symbol: :+ or :-
+      def sign
+        gain  ?  :+  :  :-
+      end
+    end
+
+    class Modification
+      VAR_MATCH_BLOCK = lambda(&:upcase)
+      STATIC_MATCH_BLOCK = lambda {|match| match }
+
+      MF = Mspire::MolecularFormula
+      OXIDIZED_METHIONINE = Modification.new('m', MF['O'], &VAR_MATCH_BLOCK)
+      # aka methylcarboxamido
+      CARBAMIDOMETHYL = Modification.new('C', MF['C2H3NO'])
+
+      DEFAULT_STATIC_MODS = [CARBAMIDOMETHYL]
+      DEFAULT_VAR_MODS = [OXIDIZED_METHIONINE]
+      DEFAULT_MODS = DEFAULT_STATIC_MODS + DEFAULT_VAR_MODS
+    end
+
+
+    Info = Struct.new(:orig_aaseq, :clean_aaseq, :formula, :penetration, :masses, :mods)
+
+    class Polynomial < Array ; end
+
+    class << self
+      # from http://rosettacode.org/wiki/Polynomial_regression#Ruby.  Returns
+      # a Polynomial object
+      def polyfit(x, y, degree)
+        x_data = x.map {|xi| (0..degree).map { |pow| (xi**pow).to_f } }
+
+        mx = Matrix[*x_data]
+        my = Matrix.column_vector(y)
+
+        Diadem::Calculator::Polynomial.new( ((mx.t * mx).inv * mx.t * my).transpose.to_a[0] )
+      end
+
+      # returns new isotopes, properly enriched.
+      def enrich_isotope(isotopes, mass_number, fraction=1.0)
+        new_isotopes = isotopes.map(&:dup)
+        leftover_fraction = 1.0 - fraction
+        new_isotopes.each {|isot| isot.relative_abundance *= leftover_fraction }
+        isot_to_enrich = new_isotopes.find {|isot| isot.mass_number == mass_number }
+        isot_to_enrich.relative_abundance += fraction
+        new_isotopes
+      end
+
+      # related intensities
+      def distributions_to_polynomials(enrichments, distributions, num=5, degree=2)
+        distributions.map {|dist| dist.intensities[0,num] }.transpose.each_with_index.map do |ar, m|
+          polyfit(enrichments, ar, degree)
+        end
+      end
+    end
+
+    # returns spectra objects.  The isotope_table handed in will not be altered
+    def initialize(element=:H, mass_number=2, penetration_table=Enrichment::AA_TABLE, isotope_table=Mspire::Isotope::BY_ELEMENT, round=false)
+      @round = round
+      @penetration_table, @element, @mass_number = penetration_table, element, mass_number
+      @isotope_table = dup_isotope_table(isotope_table)
+    end
+
+    def dup_isotope_table(table)
+      table.each.with_object({}) do |(key,val), new_table|
+        new_table[key] = val.map {|obj| obj.dup }
+      end
+    end
+
+    def max_penetration_fraction(aaseq, formula)
+      penetration = aaseq.each_char.inject(0.0) do |sum, aa|
+        sum + ( @penetration_table[aa] || 0.0 )
+      end
+      penetration = penetration.round if @round
+      @info.penetration = penetration
+      penetration.to_f / formula[@element]
+    end
+
+    # returns [formula_adjusted_for_mods, aaseq_with_no_mods]
+    def calculate_formula(aaseq_with_mods, mods)
+      mods.group_by(&:char).each do |modchar, mod|
+        aaseq_with_mods.each_char do |char|
+          if char == modchar
+          end
+        end
+      end
+
+
+      Mspire::MolecularFormula.from_aaseq(aaseq)
+    end
+    
+    # Returns [distributions, info].  Interprets lowercase m as singly oxidized methionine.
+    def calculate_isotope_distributions(aaseq, enrichments, normalize_type: :total, mods: Diadem::Calculator::Modification::DEFAULT_MODS)
+      @info = Info.new
+      pct_cutoff = nil
+
+      mf = Mspire::MolecularFormula
+      aaseq_up = aaseq
+      subtract_formula = mf.new
+      add_formula = mf.new
+      matched_mods = []
+      mods.each do |mod|
+        delta_formula = mod.gain ? add_formula : subtract_formula
+        aaseq_up = aaseq_up.gsub(mod.match) do |match|
+          matched_mods << [match, mod]
+          delta_formula.add!(mod.diff_formula)
+          mod.match_block.call(match)
+        end
+      end
+      @info.mods = matched_mods
+
+      formula = mf.from_aaseq(aaseq_up)
+      formula += add_formula
+      formula -= subtract_formula
+      @info.formula = formula
+
+      max_pen_frac = max_penetration_fraction(aaseq_up, formula)
+
+      orig_isotopes = @isotope_table[@element]
+
+      distributions = enrichments.map do |enrich_frac|
+        effective_fraction = max_pen_frac * enrich_frac
+        @isotope_table[@element] = Diadem::Calculator.enrich_isotope(orig_isotopes, @mass_number, effective_fraction)
+        spectrum = formula.isotope_distribution_spectrum(normalize_type, pct_cutoff, @isotope_table)
+        @isotope_table[@element] = orig_isotopes
+        @info.masses = spectrum.mzs unless @info.masses
+        Diadem::Distribution.new( spectrum.intensities )
+      end
+      [distributions, @info]
+    end
+  end
+end
+
+
+

data/lib/diadem/cubic/commandline.rb

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+require 'optparse'
+require 'ostruct'
+
+module Diadem
+  module Cubic
+    module Commandline
+
+      class << self
+        def parse(argv)
+          make_range = ->(start,stop,step) { Range.new(start, stop).step(step) }
+
+          start = 0.0
+          stop = 0.1
+          step = 0.002
+          opt = OpenStruct.new( {
+            carbamidomethyl: true,
+            oxidized_met: true,
+            element: :H,
+            mass_number: 2,
+            range: make_range[ start, stop, step ],
+            degree: 3,
+            header: true,
+            num_isotopomers: 5,
+          } )
+                              
+          parser = OptionParser.new do |op|
+            prog = File.basename($0)
+            op.banner =  "usage: #{prog} <AASEQ> ..." 
+            op.separator "   or: #{prog} <aaseqs>.csv" 
+            op.separator "       <aaseqs>.csv is a single column of AA sequences (no header)"
+            op.separator ""
+            op.separator "output: tab delimited to stdout if AASEQ"
+            op.separator "        <aaseqs>#{Diadem::Cubic::FILE_EXT} if csv input"
+            op.separator ""
+            op.separator "options:"
+            op.on("-e", "--element <#{opt.element}>", "element with isotopic label") {|v| opt.element = v.to_sym }
+            op.on("-m", "--mass-number <#{opt.mass_number}>", Integer, "the labeled element mass number") {|v| opt.mass_number = v }
+            op.on("--no-carbamidomethyl", "do not use this mod by default") { opt.carbamidomethyl = false }
+            op.on("--range <start:stop:step>", "the underlying input values (#{[start, stop, step].join(':')})") {|v| opt.range = make_range[ *v.split(':') ] }
+            op.on("--degree <#{opt.degree}>", Integer, "the degree polynomial") {|v| opt.degree = v }
+            op.on("--num-isotopomers <#{opt.num_isotopomers}>", Integer, "the number of isotopomers to calculate") {|v| opt.num_isotopomers = v }
+            op.on("--no-header", "don't print a header line") {|v| opt.header = false }
+          end
+          parser.parse!(argv)
+          if argv.size == 0
+            puts parser
+            exit
+          end
+          [argv, opt]
+        end
+      end
+
+    end
+  end
+end

data/lib/diadem/cubic.rb

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+require 'diadem/cubic/commandline'
+require 'diadem/calculator'
+require 'csv'
+
+module Diadem
+  module Cubic
+    
+    Isotope = Struct.new(:element, :mass_number)
+    Peptide = Struct.new(:aaseq, :isotope, :enrichments)
+    Enrichment = Struct.new(:fraction, :distribution)
+  
+    FILE_EXT = '.cubic.csv'
+    class << self
+      # returns the filename of the output if given a filename, or nil
+      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|
+            (opt.degree).downto(0) do |coeff|
+              cats << [label, "coeff", coeff].join("_")
+            end
+          end
+          out.puts cats.join(opt.delim)
+        end
+
+        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
+
+
+          (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|
+            line.push *coeffs.reverse
+          end
+          out.puts line.join(opt.delim)
+        end
+        if out.respond_to?(:path)
+          out.close
+          out.path
+        end
+      end
+
+      def is_filename?(arg)
+        arg.include?('.') 
+      end
+    end
+  end
+
+end

data/lib/diadem/distribution.rb

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+
+module Diadem
+  class Distribution
+    attr_accessor :intensities
+
+    def initialize(intensities)
+      @intensities = intensities
+    end
+
+    # returns self
+    def resize!(num)
+      newar = @intensities.dup
+      to_pad = num - @intensities.size
+      unless to_pad <= 0
+        to_pad.times { newar << 0.0 }
+      end
+      @intensities.replace( newar[0,num] )
+      self
+    end
+  end
+end

data/lib/diadem/enrichment.rb

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+
+module Diadem
+  module Enrichment
+    AA_TABLE = {
+      'A' => 4,
+      'R' => 3.43,
+      'N' => 1.89,
+      'D' => 1.89,
+      'C' => 1.62,
+      'E' => 3.95,
+      'Q' => 3.95,
+      'G' => 2.06,
+      'H' => 2.88,
+      'I' => 1,
+      'L' => 0.6,
+      'K' => 0.54,
+      'M' => 1.12,
+      'F' => 0.32,
+      'P' => 2.59,
+      'S' => 2.61,
+      'T' => 0.2,
+      'Y' => 0.42,
+      'W' => 0.0,
+      'V' => 0.56,
+    }
+  end
+end
+
+
+

data/lib/diadem/isotope_distribution.rb

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+require 'mspire/molecular_formula'
+require 'mspire/isotope'
+require 'fftw3'
+
+module Diadem
+
+  class IsotopeDistribution
+    DEFAULT_ISOTOPE_TABLE = Mspire::Isotope::BY_ELEMENT
+
+    # should always add up to 1
+    attr_accessor :intensities
+    # should be inclusive of last value
+    attr_accessor :nucleon_start
+    def initialize(intensities=[], nucleon_start=0)
+      @intensities, @nucleon_start = intensities, nucleon_start
+    end
+
+    def nucleon_end
+      nucleon_start + intensities.size - 1
+    end
+
+    class << self
+
+      def from_formula(formula)
+        Mspire::MolecularFormula[formula].isotope_distribution
+      end
+
+      # returns a new distribution, uses equal weights if none given
+      def average(distributions, weights=nil)
+        weights ||= Array.new(distributions.size, 1)
+        min_nucleon_num = distributions.map(&:nucleon_start).min
+        max_nucleon_num = distributions.map(&:nucleon_end).max
+
+        new_intensity_arrays = distributions.zip(weights).map do |dist, weight|
+          new_pcts = dist.intensities.dup
+          right_pad = max_nucleon_num - dist.nucleon_end
+          left_pad = dist.nucleon_start - min_nucleon_num
+          [[right_pad, new_pcts.size], [left_pad, 0]].each do |pad, loc|
+            new_pcts[loc,0] = Array.new(pad, 0.0)
+          end
+          new_pcts.map! {|v| v * weight }
+          new_pcts
+        end
+
+        summed_intensities = new_intensity_arrays.transpose.map do |col|
+          col.reduce(:+)
+        end
+
+        new_dist = self.new(summed_intensities, min_nucleon_num)
+        new_dist.normalize!
+      end
+    end
+
+    # normalizes intensity values and returns self
+    def normalize!(normalize_to=1.0)
+      sum = intensities.reduce(:+)
+      intensities.map! {|v| (v.to_f/sum)*normalize_to }
+      self
+    end
+
+  end
+
+end

data/lib/diadem/isotope_incorporation_table.rb

@@ -0,0 +1,6 @@
+module Diadem
+  class IsotopeIncorporationTable
+    def initialize(element, isotope)
+    end
+  end
+end

data/lib/diadem/version.rb

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+module Diadem
+  VERSION = "0.0.2"
+end

data/spec/diadem/calculator_spec.rb

@@ -0,0 +1,94 @@
+require 'spec_helper'
+require 'csv'
+
+require 'diadem/calculator'
+
+Isotope = Struct.new(:element, :mass_number)
+Peptide = Struct.new(:aaseq, :isotope, :enrichments)
+Enrichment = Struct.new(:fraction, :distribution)
+
+# returns [fractions, [array_of_intensity1s, array_of_intensity2s ...]
+def transpose_enrichments(peptide)
+  fractions = peptide.enrichments.map(&:fraction)
+  [fractions, peptide.enrichments.map(&:distribution).transpose]
+end
+
+
+describe 'calculating enrichments' do
+
+  it 'makes distributions' do
+
+    rows = CSV.read("gold_standards/output_tabular.csv")
+    mida_peptides = []
+    read_enrichments = false
+    rows.each_with_index do |row,i|
+      if row.compact.size == 0
+        read_enrichments = false
+      elsif read_enrichments
+        row.map!(&:to_f)
+        mida_peptides.last.enrichments << Enrichment.new( row[0], row[1..-1] )
+      elsif row[0] =~ /\AIsotope=/
+        (mass_number_s, element_s) = row[0].split('=').last.each_char.to_a
+        isotope = Isotope.new(element_s.to_sym, mass_number_s.to_i)
+        aaseq = rows[i-1].first.split(/\s+/).first
+        mida_peptides << Peptide.new(aaseq, isotope, [])
+        read_enrichments = true
+      end
+    end
+    #mida_peptides.reject! {|me| me.aaseq.include?('m') }
+
+    [true, false].each do |round|
+      my_peptides = mida_peptides.map do |mida_peptide|
+
+        (element, mass_number) = mida_peptide.isotope.values
+
+        calc = Diadem::Calculator.new(element, mass_number, Diadem::Enrichment::AA_TABLE, Mspire::Isotope::BY_ELEMENT, round)
+        fractions = mida_peptide.enrichments.map(&:fraction)
+        (distributions, info) = calc.calculate_isotope_distributions(mida_peptide.aaseq, fractions)
+
+        my_peptide = Peptide.new( mida_peptide.aaseq, mida_peptide.isotope )
+        my_peptide.enrichments = distributions.zip(fractions).map do |distribution, fractions|
+          Enrichment.new( fractions, distribution.resize!(7) )
+        end
+        my_peptide
+      end
+
+      $PLOT = false
+      if $PLOT
+        require 'gnuplot'
+        mida_peptides.zip(my_peptides) do |mida, mine|
+          plottype = 'png'
+          base = mida.aaseq + "-ROUND:#{round}"
+          plotfile = base + ".#{plottype}"
+          mi = mida.isotope
+
+          Gnuplot.open do |gp|
+            Gnuplot::Plot.new(gp) do |plot|
+
+              plot.title [mida.aaseq, "el:#{mi.element}", "massnum:#{mi.mass_number}", "round:#{round}"].join(" ")
+              plot.terminal plottype
+              plot.output plotfile
+              plot.xlabel "label fraction"
+              plot.ylabel "relative intensity"
+              plot.yrange "[0:0.5]"
+
+              plot.data = []
+
+              mida_fracs_and_int_ars = transpose_enrichments(mida)
+
+              byu_fracs_and_ints_ars = transpose_enrichments(mine)
+              [:mida, mida_fracs_and_int_ars, :byu, byu_fracs_and_ints_ars].each_slice(2) do |name, (fracs, int_ars)|
+                int_ars.each_with_index do |ints, mnum|
+                  plot.data << Gnuplot::DataSet.new( [fracs, ints] ) {|ds| ds.title = "#{name}-M#{mnum}"; ds.with = "lines" }
+                end
+              end
+            end
+          end
+        end
+      end
+
+    end
+  end
+end
+
+

data/spec/diadem/cubic_spec.rb

@@ -0,0 +1,26 @@
+require 'spec_helper'
+require 'csv'
+
+require 'diadem/cubic'
+
+describe Diadem::Cubic do
+  specify 'using an input file' do
+    filename = Diadem::Cubic.run( [TESTFILES + "/input.csv"], )
+    File.basename(filename).should == 'input.cubic.csv' 
+    rows = CSV.read(filename)
+    rows.first.should == %w(sequence mods formula mass n M0 M1 M2 M3 M4 M0_coeff_3 M0_coeff_2 M0_coeff_1 M0_coeff_0 M1_coeff_3 M1_coeff_2 M1_coeff_1 M1_coeff_0 M2_coeff_3 M2_coeff_2 M2_coeff_1 M2_coeff_0 M3_coeff_3 M3_coeff_2 M3_coeff_1 M3_coeff_0 M4_coeff_3 M4_coeff_2 M4_coeff_1 M4_coeff_0)
+    rows.size.should == 4
+    lrow = rows.last
+    # these are verified
+    lrow[0,10].should == ["NEVHCmLGQSTCEMIR", "C:+C2H3NO C:+C2H3NO m:+O", "C77H129N25O28S4", "1979.832173", "32.56", "0.298777", "0.293168", "0.213061", "0.114555", "0.051392"]
+    # the below values are not verified for complete accuracy, but are frozen.
+    # I *have* verified that my polyfit gives exactly the same as numpy.polyfit
+    # I *have* verified that my fits give nearly the identical result when the
+    # formula is used to calculate the function and compared with the raw
+    # data.
+    coeff_exp = ["-392.23934817385657", "96.69007230820951", "-8.611345775533028", "0.2941872043446288", "274.6030329923823", "-32.519634396959496", "-1.9819130901305437", "0.3015660872075071", "349.4058191339298", "-74.1471126522828", "2.8594996757768354", "0.2129971981087685", "101.51558561078951", "-45.23875117790308", "3.95095594421288", "0.1114045333664326", "-125.24493326823091", "0.15596911712410133", "2.5230711874760186", "0.04912040472741169"]
+    lrow[10..-1].zip( coeff_exp )  do |mine, csv|
+      mine.to_f.should be_within(1e-5).of(csv.to_f)
+    end
+  end
+end

data/spec/diadem/isotope_distribution_spec.rb

@@ -0,0 +1,40 @@
+require 'spec_helper'
+
+require 'diadem/isotope_distribution'
+
+
+#describe Diadem::IsotopeDistribution do
+  #before do
+    #@dists = 
+      #[[1,2,1], 1,
+       #[2, 1, 1], 2,
+       #[4], 6
+    #].each_slice(2).map do |ints, start|
+      #Diadem::IsotopeDistribution.new( ints, start ).normalize!
+    #end
+  #end
+
+  #specify 'average with equal weights' do
+    #output = Diadem::IsotopeDistribution.average(@dists)
+    #[0.083, 0.333, 0.167, 0.083, 0.0, 0.333].zip(output.intensities) do |act, exp|
+      #act.should be_within(0.002).of(exp)
+    #end
+    #output.nucleon_start.should == 1
+    #output.nucleon_end.should == 6
+  #end
+
+  #specify 'average with unequal weights' do
+    #output = Diadem::IsotopeDistribution.average(@dists, [1,1,10])
+    #[0.021, 0.083, 0.042, 0.021, 0.0, 0.833].zip(output.intensities) do |act, exp|
+      #act.should be_within(0.002).of(exp)
+    #end
+    #output.nucleon_start.should == 1
+    #output.nucleon_end.should == 6
+  #end
+
+  #specify 'normalize!' do
+    #output = Diadem::IsotopeDistribution.new([2,2,2,2], 3).normalize!
+    #output.nucleon_start.should == 3
+    #output.intensities.should == [0.25, 0.25, 0.25, 0.25]
+  #end
+#end

data/spec/spec_helper.rb

@@ -0,0 +1,27 @@
+require 'simplecov'
+SimpleCov.start
+
+require 'rspec'
+
+require 'rspec/core/formatters/progress_formatter'
+# doesn't say so much about pending guys
+class QuietPendingFormatter < RSpec::Core::Formatters::ProgressFormatter
+  def example_pending(example)
+    output.print pending_color('*')
+  end
+end
+
+require 'rspec/core/formatters/documentation_formatter'
+class QuietPendingDocFormatter < RSpec::Core::Formatters::DocumentationFormatter
+  def example_pending(example)
+    output.puts pending_color( "<pending>: #{example.execution_result[:pending_message]}" )
+  end
+end
+
+RSpec.configure do |config|
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+  config.formatter = QuietPendingDocFormatter
+  config.color = true
+end
+
+TESTFILES = File.dirname(__FILE__) + "/testfiles"

data/spec/testfiles/input.csv

@@ -0,0 +1,3 @@
+LGADmEDLR,
+NEVHTMLGQSTEEIR,
+NEVHCmLGQSTCEMIR,

data/spec/testfiles/input.cubic.csv

@@ -0,0 +1,4 @@
+sequence,mods,formula,mass,n,M0,M1,M2,M3,M4,M0_coeff_3,M0_coeff_2,M0_coeff_1,M0_coeff_0,M1_coeff_3,M1_coeff_2,M1_coeff_1,M1_coeff_0,M2_coeff_3,M2_coeff_2,M2_coeff_1,M2_coeff_0,M3_coeff_3,M3_coeff_2,M3_coeff_1,M3_coeff_0,M4_coeff_3,M4_coeff_2,M4_coeff_1,M4_coeff_0
+LGADmEDLR,m:+O,C41H70N12O17S,1034.47026,19.540000000000003,0.556753,0.283781,0.115285,0.033992,0.008188,-271.9669543025388,83.87707865863915,-10.465171001547173,0.5549760242624675,447.26750757706844,-95.6467773946335,4.1767024133301724,0.2886473523635921,6.84299765300193,-28.68989673734115,4.13419674326592,0.11197392177809003,-142.35794452920663,15.157584520461455,1.7045563652845814,0.03326539309479602,-77.519961106925,17.24516248866918,0.37336969361968486,0.008718956309883851
+NEVHTMLGQSTEEIR,,C71H118N22O27S,1742.825748,32.35,0.377313,0.332051,0.182291,0.074572,0.024703,-489.95684055041977,121.08399596787066,-10.824527731710008,0.3716306301733113,396.4694223063598,-53.6786513841365,-1.3631060138342357,0.34307099404888625,463.833104592279,-104.37963257827352,5.26331279186841,0.18182473265187887,26.202644313310657,-39.45052607309262,4.745738877395441,0.0692194335651921,-228.23593191536418,19.192095667466113,2.023880307456716,0.022424872233935855
+NEVHCmLGQSTCEMIR,C:+C2H3NO C:+C2H3NO m:+O,C77H129N25O28S4,1979.832173,32.56,0.298777,0.293168,0.213061,0.114555,0.051392,-392.23934817385657,96.69007230820951,-8.611345775533028,0.2941872043446288,274.6030329923823,-32.519634396959496,-1.9819130901305437,0.3015660872075071,349.4058191339298,-74.1471126522828,2.8594996757768354,0.2129971981087685,101.51558561078951,-45.23875117790308,3.95095594421288,0.1114045333664326,-125.24493326823091,0.15596911712410133,2.5230711874760186,0.04912040472741169

metadata

@@ -0,0 +1,187 @@
+--- !ruby/object:Gem::Specification
+name: diadem
+version: !ruby/object:Gem::Version
+  version: 0.0.2
+platform: ruby
+authors:
+- John Prince
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-09-11 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: mspire
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.10.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.10.0
+- !ruby/object:Gem::Dependency
+  name: fftw3
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.3'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.13.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.13.0
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: gnuplot
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.6.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.6.2
+description: Dynamic isotope analysis for mass spectrometry isotope experiments.  Calculates
+  and visualizes varying isotope ratios and allows the user fine control over incorporation
+  rates.
+email:
+- jtprince@gmail.com
+executables:
+- diadem-cubic.rb
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/diadem-cubic.rb
+- diadem.gemspec
+- lib/diadem/calculator.rb
+- lib/diadem/cubic.rb
+- lib/diadem/cubic/commandline.rb
+- lib/diadem/distribution.rb
+- lib/diadem/enrichment.rb
+- lib/diadem/isotope_distribution.rb
+- lib/diadem/isotope_incorporation_table.rb
+- lib/diadem/version.rb
+- spec/diadem/calculator_spec.rb
+- spec/diadem/cubic_spec.rb
+- spec/diadem/isotope_distribution_spec.rb
+- spec/spec_helper.rb
+- spec/testfiles/input.csv
+- spec/testfiles/input.cubic.csv
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.3
+signing_key: 
+specification_version: 4
+summary: Dynamic isotope analysis for mass spectrometry isotope experiments
+test_files:
+- spec/diadem/calculator_spec.rb
+- spec/diadem/cubic_spec.rb
+- spec/diadem/isotope_distribution_spec.rb
+- spec/spec_helper.rb
+- spec/testfiles/input.csv
+- spec/testfiles/input.cubic.csv
+has_rdoc: