mspire-simulator 0.1.0

data/mspire-simulator.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "mspire-simulator"
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["anoyce"]
+  s.date = "2012-08-10"
+  s.description = "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file.\n\t\t\tCan simulate specific data if given an MZML file containing a single isolated peptide peak."
+  s.email = "andrewbnoyce@gmail.com"
+  s.executables = ["mspire-simulator"]
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "bin/mspire-simulator",
+    "bin/sim_mail.rb",
+    "bin/weka/M5P.model",
+    "bin/weka/M5Rules.model",
+    "bin/weka/weka.jar",
+    "lib/ms/curvefit.rb",
+    "lib/ms/curvefit/curve_fit_helper.rb",
+    "lib/ms/curvefit/fit_graph.rb",
+    "lib/ms/curvefit/mzml_reader.rb",
+    "lib/ms/isoelectric_calc.rb",
+    "lib/ms/merger.rb",
+    "lib/ms/mzml_wrapper.rb",
+    "lib/ms/noise.rb",
+    "lib/ms/rt/rt_helper.rb",
+    "lib/ms/rt/rtgenerator.rb",
+    "lib/ms/rt/weka.rb",
+    "lib/ms/sim_digester.rb",
+    "lib/ms/sim_feature.rb",
+    "lib/ms/sim_peptide.rb",
+    "lib/ms/sim_spectra.rb",
+    "lib/ms/sim_trollop.rb",
+    "lib/ms/tr_file_writer.rb",
+    "lib/progress.rb",
+    "mspire-simulator.gemspec",
+    "spec/file_writer_spec.rb",
+    "spec/merger_spec.rb",
+    "spec/ms-simulate_spec.rb",
+    "spec/peptide_spec.rb",
+    "spec/progress_spec.rb",
+    "spec/spec_helper.rb",
+    "spec/spectra_spec.rb",
+    "testFiles/contam/hum_keratin.fasta"
+  ]
+  s.homepage = "http://dl.dropbox.com/u/42836826/Ms_Sim_Homepage.html"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.21"
+  s.summary = "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file."
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<mspire>, ["= 0.8.2"])
+      s.add_runtime_dependency(%q<rubyvis>, ["= 0.5.2"])
+      s.add_runtime_dependency(%q<nokogiri>, ["= 1.5.2"])
+      s.add_runtime_dependency(%q<ffi>, ["= 1.0.11"])
+      s.add_runtime_dependency(%q<ffi-inliner>, ["= 0.2.4"])
+      s.add_runtime_dependency(%q<fftw3>, ["= 0.3"])
+      s.add_runtime_dependency(%q<distribution>, ["= 0.7.0"])
+      s.add_runtime_dependency(%q<pony>, ["= 1.4"])
+      s.add_runtime_dependency(%q<obo>, ["= 0.1.0"])
+      s.add_runtime_dependency(%q<trollop>, ["= 1.16.2"])
+    else
+      s.add_dependency(%q<mspire>, ["= 0.8.2"])
+      s.add_dependency(%q<rubyvis>, ["= 0.5.2"])
+      s.add_dependency(%q<nokogiri>, ["= 1.5.2"])
+      s.add_dependency(%q<ffi>, ["= 1.0.11"])
+      s.add_dependency(%q<ffi-inliner>, ["= 0.2.4"])
+      s.add_dependency(%q<fftw3>, ["= 0.3"])
+      s.add_dependency(%q<distribution>, ["= 0.7.0"])
+      s.add_dependency(%q<pony>, ["= 1.4"])
+      s.add_dependency(%q<obo>, ["= 0.1.0"])
+      s.add_dependency(%q<trollop>, ["= 1.16.2"])
+    end
+  else
+    s.add_dependency(%q<mspire>, ["= 0.8.2"])
+    s.add_dependency(%q<rubyvis>, ["= 0.5.2"])
+    s.add_dependency(%q<nokogiri>, ["= 1.5.2"])
+    s.add_dependency(%q<ffi>, ["= 1.0.11"])
+    s.add_dependency(%q<ffi-inliner>, ["= 0.2.4"])
+    s.add_dependency(%q<fftw3>, ["= 0.3"])
+    s.add_dependency(%q<distribution>, ["= 0.7.0"])
+    s.add_dependency(%q<pony>, ["= 1.4"])
+    s.add_dependency(%q<obo>, ["= 0.1.0"])
+    s.add_dependency(%q<trollop>, ["= 1.16.2"])
+  end
+end
+

data/spec/file_writer_spec.rb

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+
+require 'time'
+require 'mspire'
+require 'ms/sim_spectra'
+require 'ms/sim_peptide'
+require 'ms/merger'
+
+describe MS::Txml_file_writer do
+  before(:all) do
+    peptides = []
+    peptides<<MS::Peptide.new("ANDY",1)
+    peptides<<MS::Peptide.new("PRINCE",2)
+    peptides<<MS::Peptide.new("PEPTIDE",3)
+    one_d = false
+    opts = {:sampling_rate => 1.0, :run_time => 5000.0,
+            :dropout_percentage => 0, :noise_density => 20,
+            :jagA => 10.34, :jagC => 0.00712, :jagB => 0.12,
+            :wobA => 0.001071, :wobB => -0.5430, :mu => 25.0}
+    @spectra = MS::Sim_Spectra.new(peptides,opts,one_d)
+    @features = @spectra.features
+    @file_name = Time.now.to_s
+  end
+  
+  after(:all) do
+    File.delete("#{@file_name}_truth.xml")
+  end
+  
+  it "#write Writes an XML file that includes all information for the spectra" do
+    xml = MS::Txml_file_writer.write(@features,@spectra.spectra,@file_name)
+    File.exist?("#{@file_name}_truth.xml").should == true
+    file = File.open("#{@file_name}_truth.xml","r")
+    pep_verify = []
+    file.each_line{|line| if line =~ /ANDY|PRINCE|PEPTIDE/; pep_verify<<true; end;}
+    pep_verify.should have(3).Boolean
+    pep_verify.each do |ver|
+      ver.should == true
+    end
+  end
+end
+
+
+describe MS::Tcsv_file_writer do
+  before(:all) do
+    peptides = []
+    peptides<<MS::Peptide.new("ANDY",1)
+    peptides<<MS::Peptide.new("PRINCE",2)
+    peptides<<MS::Peptide.new("PEPTIDE",3)
+    one_d = false
+    opts = {:sampling_rate => 1.0, :run_time => 5000.0,
+            :dropout_percentage => 0, :noise_density => 20,
+            :jagA => 10.34, :jagC => 0.00712, :jagB => 0.12,
+            :wobA => 0.001071, :wobB => -0.5430, :mu => 25.0}
+    @spectra = MS::Sim_Spectra.new(peptides,opts,one_d)
+    @noise = @spectra.noiseify
+    @features = @spectra.features
+    @file_name = Time.now.to_s 
+  end
+  
+  after(:all) do
+    File.delete("#{@file_name}_truth.csv")
+  end
+  
+  it "#write Writes an CSV file that includes all information for the spectra" do
+    csv = MS::Tcsv_file_writer.write(@spectra.spectra,@spectra.data,@noise,@features,@file_name)
+    r_times = MS::Sim_Spectra.r_times
+    times_ver = []
+    File.exist?("#{@file_name}_truth.csv").should == true
+    file = File.open("#{@file_name}_truth.csv","r")
+    file.each_line do |line| 
+      next if line =~ /rt/
+      r_times.include?(line.chomp.split(/,/)[0].to_f).should == true
+    end
+  end
+end

data/spec/merger_spec.rb

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+
+require 'ms/merger'
+
+describe Merger do 
+  before(:all) do 
+    @spectra = {1 => [[1.0,1.5,1.7,3.0,4.0,5.0,6.0,7.0,8.0,9.0],[10,9,8,7,6,5,4,3,2,1]], 2 => [[1,2,3,4,5,6,7,8,9],[9,8,7,6,5,4,3,2,1]]}
+  end
+  
+  it "#merge Takes spectra and a value that represents half the range where two peaks would be considered overlapping, then it merges these into meta peaks and returns the spectra" do
+    half_range = 0.5
+    meta_merged = Merger.merge(@spectra,half_range)
+    meta_merged[1].should == [[{[1.236842105263158, 52.63157894736842, 47.368421052631575]=>[1.0, 1.5]}, 1.7, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0], [[10, 9], 8, 7, 6, 5, 4, 3, 2, 1]]
+    meta_merged[2].should == [[1, 2, 3, 4, 5, 6, 7, 8, 9], [9, 8, 7, 6, 5, 4, 3, 2, 1]]
+  end 
+  
+  it "#compact Takes a meta merged spectra and removes meta data to return normal merged spectra" do
+    half_range = 0.5
+    meta_merged = Merger.merge(@spectra,half_range)
+    merged = Merger.compact(meta_merged)
+    merged[1].should == [[1.236842105263158, 1.7, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0], [19, 8, 7, 6, 5, 4, 3, 2, 1]]
+    merged[2].should == [[1, 2, 3, 4, 5, 6, 7, 8, 9], [9, 8, 7, 6, 5, 4, 3, 2, 1]]
+  end
+end

data/spec/ms-simulate_spec.rb

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+$LOAD_PATH << './lib'
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "MSsimulate" do
+  it "Gathers parameters from the cmd line and runs the simulator; If no params are given or --help a help message is displayed" do
+    output = `ruby bin/ms-simulate.rb --help`
+    output.should =~ /where/
+  end
+end

data/spec/peptide_spec.rb

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+#peptide_spec.rb
+
+require 'mspire'
+require 'ms/sim_peptide'
+
+describe MS::Peptide do
+  it "Creates a peptide object given an amino acid sequence and charge state" do 
+    pep = MS::Peptide.new("HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNR",2)
+    pep.should be_a(MS::Peptide)
+    pep.sequence.should == "HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNR"
+    pep.mono_mz.should == 1939.3147555802952
+    #Contains the core theoretical spectrum
+    pep.core_mzs[0].round.should == 1938
+    pep.core_ints[0].round.should == 42
+  end
+end

data/spec/progress_spec.rb

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+#progress_spec.rb
+
+require 'progress'
+require 'time'
+
+describe Progress, "#progress" do
+  it "Prints out a given message and percentage, refreshing the current line with each call." do
+    101.times do |i|
+      Progress.progress("Message:",i)
+      sleep 0.01
+    end
+  end
+  
+  it "Also can take a final time to show how long a process took." do 
+    start = Time.now
+    101.times do |i|
+      Progress.progress("Message:",i)
+      sleep 0.01
+    end
+    Progress.progress("Message:",100,Time.now - start)
+  end
+end 

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

data/spec/spectra_spec.rb

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+#spectra_spec.rb
+
+require 'mspire'
+require 'ms/sim_spectra'
+require 'ms/sim_peptide'
+
+describe MS::Sim_Spectra do
+  before(:all) do 
+    peptides = []
+    peptides<<MS::Peptide.new("ANDY",1)
+    peptides<<MS::Peptide.new("PRINCE",2)
+    peptides<<MS::Peptide.new("PEPTIDE",3)
+    one_d = false
+    opts = {:sampling_rate => 1.0, :run_time => 5000.0,
+            :dropout_percentage => 0, :noise_density => 20,
+            :jagA => 10.34, :jagC => 0.00712, :jagB => 0.12,
+            :wobA => 0.001071, :wobB => -0.5430, :mu => 25.0}
+    @spectra = MS::Sim_Spectra.new(peptides,opts,one_d)
+    @features = @spectra.features
+  end
+  
+  it "Creates spectra for a ms run given an array of peptide objects, a sampling rate and a run time, " do
+    @spectra.should be_a(MS::Sim_Spectra)
+  end
+  
+  it "#data Returns a hash that has retention times as keys and arrays as values such that [[mzs],[intensitys]]" do 
+    @spectra.data.should be_a(Hash)
+  end
+  
+  it "#max_mz Returns the maximum of all the m/z values" do
+    (485..487).should cover(@spectra.max_mz)
+  end
+  
+  it "#noiseify Creates and returns the hash that represents the noise of the spectra" do
+    noise = @spectra.noiseify
+    noise.should be_a(Hash)
+  end
+  
+  it "#spectra Returns a hash with all data including noise if turned on" do 
+    @spectra.spectra.should be_a(Hash)
+  end
+  
+  it "#features Returns complete features" do
+    @spectra.features
+    @spectra.features.should have(3).peptides
+  end
+  
+#FEATURES---------------------------------------------------------------
+  
+  it "Each feature should have a sequence" do 
+    seqs = ["ANDY","PRINCE","PEPTIDE"]
+    @features.each_with_index do |fe,i|
+      fe.sequence.should == seqs[i]
+    end
+  end
+  
+  it "Each feature should have a mass" do 
+    masses = [481,730,799]
+    @spectra.features.each_with_index do |fe,i|
+      fe.mass.round.should == masses[i]
+    end
+  end
+  
+  it "Each feature should have a charge" do 
+    charges = [1,2,3]
+    @spectra.features.each_with_index do |fe,i|
+      fe.charge.should == charges[i]
+    end
+  end
+  
+  it "Each feature should have a monoisotopic m/z" do 
+    mono_mzs = [481,365,266]
+    @spectra.features.each_with_index do |fe,i|
+      fe.mono_mz.round.should == mono_mzs[i]
+    end
+  end
+  
+  it "Each feature should have a theoretical spectrum" do 
+    andy_spec = [[481, 482, 483, 484, 485, 486],
+                 [100, 24, 5, 1, 0, 0]]
+    prince_spec = [[365, 366, 366, 367, 367, 368, 368, 369],
+                 [100, 37, 13, 3, 1, 0, 0, 0]]
+    peptide_spec = [[266, 267, 267, 267, 268, 268, 268],
+                 [100, 41, 11, 2, 0, 0, 0]]
+    specs = [andy_spec,prince_spec,peptide_spec]
+    
+    @spectra.features.each_with_index do |fe,i|
+      test = [fe.core_mzs.map{|mz| mz.round},fe.core_ints.map{|int| int.round}]
+      test.should == specs[i]
+    end
+  end
+  
+  it "Each feature should have a predicted retention time and intensity" do 
+      p_rts = [(2079..2082),(1774..1777),(1400..1402)]
+      p_ints = [2.325,2.927,3.559]
+    @spectra.features.each_with_index do |fe,i|
+      p_rts[i].should cover(fe.p_rt)
+      fe.p_int.should == p_ints[i]
+    end
+  end
+  
+  it "Each feature should have amino acid counts" do 
+    counts = [[1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0.0],
+              [0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0.0],
+              [0, 0, 0, 1, 0, 0, 2, 0, 0, 0, 0, 1, 0, 0, 0, 0, 2, 0, 1, 0, 0, 0, 0, 0.0]]
+    @spectra.features.each_with_index do |fe,i|
+      fe.aa_counts.should == counts[i]
+    end
+  end
+  
+end

data/testFiles/contam/hum_keratin.fasta

@@ -0,0 +1,11 @@
+>gi|18031719|gb|AY033495.1| Homo sapiens keratin protein K6irs (KRT6) mRNA, translated
+MSRQLTHFPRGERLGFSGCSAVLSGGIGSSSASFRARVKGSASF
+GSKSLSCLGGSRSLALSAAARRGGGRLGGFVGTAFGSAGLGPKCPSVCPPGGIPQVTV
+NKSLLAPLNVEMDPEIQRVRAQEREQIKALNNKFASFIDKVRFLEQQNQVLETKWNLL
+QQLDLNNCRKNLEPIYEGYISNLQKQLEMLSGDGVRLDSELRNMQDLVEDYKKRYEVE
+INRRTAAENEFVVLKKDVDAAYMNKVELQAKVDSLTDEIKFFKCLYEGEITQIQSHIS
+DTSIVLSMDNNRDLDLDSIIAEVRAQYEEIALKSKAEAETLYQTKIQELQVTAGQHGD
+DLKLTKAEISELNRLIQRIRSEIGNVKKCADLETAIADAEQRGDCALKDARAKLDELE
+GALHQAKEELARMLREYQELVSLKLALDMEIATYRKLLESEECRMSGEYPNSVSISVI
+SSTNAGAGGAGFSMGFGASSSYSYKTAAADVKTKGSCGSELKDPLAKTSGSSCATKKA
+SR

metadata

@@ -0,0 +1,246 @@
+--- !ruby/object:Gem::Specification
+name: mspire-simulator
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- anoyce
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-08-10 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: mspire
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.8.2
+- !ruby/object:Gem::Dependency
+  name: rubyvis
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.5.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.5.2
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.5.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.5.2
+- !ruby/object:Gem::Dependency
+  name: ffi
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.0.11
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.0.11
+- !ruby/object:Gem::Dependency
+  name: ffi-inliner
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.2.4
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.2.4
+- !ruby/object:Gem::Dependency
+  name: fftw3
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: '0.3'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: '0.3'
+- !ruby/object:Gem::Dependency
+  name: distribution
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.7.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.7.0
+- !ruby/object:Gem::Dependency
+  name: pony
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: obo
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+- !ruby/object:Gem::Dependency
+  name: trollop
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.16.2
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 1.16.2
+description: ! "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file.\n\t\t\tCan
+  simulate specific data if given an MZML file containing a single isolated peptide
+  peak."
+email: andrewbnoyce@gmail.com
+executables:
+- mspire-simulator
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/mspire-simulator
+- bin/sim_mail.rb
+- bin/weka/M5P.model
+- bin/weka/M5Rules.model
+- bin/weka/weka.jar
+- lib/ms/curvefit.rb
+- lib/ms/curvefit/curve_fit_helper.rb
+- lib/ms/curvefit/fit_graph.rb
+- lib/ms/curvefit/mzml_reader.rb
+- lib/ms/isoelectric_calc.rb
+- lib/ms/merger.rb
+- lib/ms/mzml_wrapper.rb
+- lib/ms/noise.rb
+- lib/ms/rt/rt_helper.rb
+- lib/ms/rt/rtgenerator.rb
+- lib/ms/rt/weka.rb
+- lib/ms/sim_digester.rb
+- lib/ms/sim_feature.rb
+- lib/ms/sim_peptide.rb
+- lib/ms/sim_spectra.rb
+- lib/ms/sim_trollop.rb
+- lib/ms/tr_file_writer.rb
+- lib/progress.rb
+- mspire-simulator.gemspec
+- spec/file_writer_spec.rb
+- spec/merger_spec.rb
+- spec/ms-simulate_spec.rb
+- spec/peptide_spec.rb
+- spec/progress_spec.rb
+- spec/spec_helper.rb
+- spec/spectra_spec.rb
+- testFiles/contam/hum_keratin.fasta
+homepage: http://dl.dropbox.com/u/42836826/Ms_Sim_Homepage.html
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.21
+signing_key: 
+specification_version: 3
+summary: Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file.
+test_files: []