mspire-simulator 0.2.1 → 0.3.0

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Files changed (18) hide show
  1. data/README.rdoc +11 -8
  2. data/Rakefile +2 -1
  3. data/VERSION +1 -1
  4. data/bin/mspire-simulator +49 -48
  5. data/lib/ms/merger.rb +20 -59
  6. data/lib/ms/mzml_wrapper.rb +60 -40
  7. data/lib/ms/noise.rb +1 -1
  8. data/lib/ms/rt/rtgenerator.rb +33 -30
  9. data/lib/ms/rt/weka.rb +16 -12
  10. data/lib/ms/sim_digester.rb +37 -62
  11. data/lib/ms/sim_feature.rb +58 -151
  12. data/lib/ms/sim_modifications.rb +40 -0
  13. data/lib/ms/sim_peptide.rb +61 -103
  14. data/lib/ms/sim_spectra.rb +17 -31
  15. data/lib/ms/sim_trollop.rb +9 -4
  16. data/lib/ms/tr_file_writer.rb +34 -151
  17. data/mspire-simulator.gemspec +9 -5
  18. metadata +21 -4
data/mspire-simulator.gemspec CHANGED
@@ -5,11 +5,11 @@
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  Gem::Specification.new do |s|
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  s.name = "mspire-simulator"
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- s.version = "0.2.1"
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+ s.version = "0.3.0"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["anoyce"]
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- s.date = "2012-12-14"
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+ s.date = "2012-12-28"
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  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."
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  s.email = "andrewbnoyce@gmail.com"
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  s.executables = ["mspire-simulator", "sim_mail"]
@@ -38,6 +38,7 @@ Gem::Specification.new do |s|
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  "lib/ms/rt/weka.rb",
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  "lib/ms/sim_digester.rb",
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  "lib/ms/sim_feature.rb",
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+ "lib/ms/sim_modifications.rb",
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  "lib/ms/sim_peptide.rb",
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  "lib/ms/sim_spectra.rb",
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  "lib/ms/sim_trollop.rb",
@@ -63,7 +64,7 @@ Gem::Specification.new do |s|
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  s.specification_version = 3
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  if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
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- s.add_runtime_dependency(%q<mspire>, ["= 0.8.2"])
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+ s.add_runtime_dependency(%q<mspire>, ["= 0.8.5"])
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  s.add_runtime_dependency(%q<rubyvis>, ["= 0.5.2"])
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  s.add_runtime_dependency(%q<nokogiri>, ["= 1.5.2"])
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  s.add_runtime_dependency(%q<ffi>, ["= 1.0.11"])
@@ -74,8 +75,9 @@ Gem::Specification.new do |s|
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  s.add_runtime_dependency(%q<obo>, ["= 0.1.0"])
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  s.add_runtime_dependency(%q<trollop>, ["= 1.16.2"])
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  s.add_runtime_dependency(%q<MS-fragmenter>, ["= 0.0.2"])
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+ s.add_runtime_dependency(%q<sqlite3>, ["= 1.3.6"])
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  else
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- s.add_dependency(%q<mspire>, ["= 0.8.2"])
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+ s.add_dependency(%q<mspire>, ["= 0.8.5"])
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  s.add_dependency(%q<rubyvis>, ["= 0.5.2"])
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  s.add_dependency(%q<nokogiri>, ["= 1.5.2"])
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  s.add_dependency(%q<ffi>, ["= 1.0.11"])
@@ -86,9 +88,10 @@ Gem::Specification.new do |s|
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  s.add_dependency(%q<obo>, ["= 0.1.0"])
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  s.add_dependency(%q<trollop>, ["= 1.16.2"])
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  s.add_dependency(%q<MS-fragmenter>, ["= 0.0.2"])
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+ s.add_dependency(%q<sqlite3>, ["= 1.3.6"])
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  end
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  else
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- s.add_dependency(%q<mspire>, ["= 0.8.2"])
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+ s.add_dependency(%q<mspire>, ["= 0.8.5"])
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  s.add_dependency(%q<rubyvis>, ["= 0.5.2"])
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  s.add_dependency(%q<nokogiri>, ["= 1.5.2"])
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  s.add_dependency(%q<ffi>, ["= 1.0.11"])
@@ -99,6 +102,7 @@ Gem::Specification.new do |s|
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  s.add_dependency(%q<obo>, ["= 0.1.0"])
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  s.add_dependency(%q<trollop>, ["= 1.16.2"])
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  s.add_dependency(%q<MS-fragmenter>, ["= 0.0.2"])
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+ s.add_dependency(%q<sqlite3>, ["= 1.3.6"])
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  end
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  end
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metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: mspire-simulator
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  version: !ruby/object:Gem::Version
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- version: 0.2.1
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+ version: 0.3.0
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  prerelease:
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  platform: ruby
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  authors:
@@ -9,7 +9,7 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2012-12-14 00:00:00.000000000 Z
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+ date: 2012-12-28 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: mspire
@@ -18,7 +18,7 @@ dependencies:
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  requirements:
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  - - '='
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  - !ruby/object:Gem::Version
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- version: 0.8.2
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+ version: 0.8.5
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -26,7 +26,7 @@ dependencies:
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  requirements:
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  - - '='
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  - !ruby/object:Gem::Version
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- version: 0.8.2
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+ version: 0.8.5
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  - !ruby/object:Gem::Dependency
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  name: rubyvis
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  requirement: !ruby/object:Gem::Requirement
@@ -187,6 +187,22 @@ dependencies:
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  - - '='
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  - !ruby/object:Gem::Version
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  version: 0.0.2
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+ - !ruby/object:Gem::Dependency
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+ name: sqlite3
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - '='
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+ - !ruby/object:Gem::Version
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+ version: 1.3.6
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - '='
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+ - !ruby/object:Gem::Version
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+ version: 1.3.6
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  description: ! "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML file.\n\t\t\tCan
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  simulate specific data if given an MZML file containing a single isolated peptide
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  peak."
@@ -219,6 +235,7 @@ files:
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  - lib/ms/rt/weka.rb
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  - lib/ms/sim_digester.rb
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  - lib/ms/sim_feature.rb
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+ - lib/ms/sim_modifications.rb
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  - lib/ms/sim_peptide.rb
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  - lib/ms/sim_spectra.rb
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  - lib/ms/sim_trollop.rb