mspire-simulator 0.1.1 → 0.1.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/README.rdoc +1 -1
- data/Rakefile +1 -1
- data/VERSION +1 -1
- data/bin/mspire-simulator +2 -2
- data/bin/{sim_mail.rb → sim_mail} +0 -0
- data/lib/ms/rt/weka.rb +8 -2
- data/{bin → lib}/weka/M5P.model +0 -0
- data/{bin → lib}/weka/M5Rules.model +0 -0
- data/mspire-simulator.gemspec +5 -6
- metadata +5 -5
- data/bin/weka/weka.jar +0 -0
data/README.rdoc
CHANGED
@@ -7,7 +7,7 @@ Description:
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gem install mspire-simulator
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Dependencies:
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ruby 1.9*
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-
weka 3.6.0
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+
weka 3.6.0 - May need to add to CLASSPATH see: http://weka.wikispaces.com/CLASSPATH+problems
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fftw 3.2.2 - Tested in Linux Mint 12 and Ubuntu Oneiric Ocelot
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== Examples
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data/Rakefile
CHANGED
@@ -24,7 +24,7 @@ Jeweler::Tasks.new do |gem|
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gem.add_dependency "obo", "= 0.1.0"
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gem.add_dependency "trollop", "= 1.16.2"
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gem.executables = ["mspire-simulator"]
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gem.executables = ["mspire-simulator","sim_mail"]
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gem.files.exclude "elution_curvefit.svg"
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gem.files.exclude "intensity_var_curvefit.svg"
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gem.files.exclude "lib/pool.rb"
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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.1.
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0.1.2
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data/bin/mspire-simulator
CHANGED
@@ -120,8 +120,8 @@ module MspireSimulator
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end
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puts "Exception - Simulation Failed"
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system "
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system "sim_mail #{email} Exception - Simulation Failed" if email != "nil"
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else
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system "
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system "sim_mail #{email} Success! - Simulation Complete" if email != "nil"
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end
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end
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File without changes
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data/lib/ms/rt/weka.rb
CHANGED
@@ -13,7 +13,10 @@ module MS
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data<<pep.aa_counts
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end
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arff = make_rt_arff(Time.now.nsec.to_s,data)
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path = Gem.bin_path('mspire-simulator', 'mspire-simulator').split(/\//)
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dir = path[0..path.size-3].join("/")
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system("java weka.classifiers.functions.MultilayerPerceptron -T #{arff} -l #{dir}/lib/weka/M5Rules.model -p 24 > #{arff}.out")
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system("rm #{arff}")
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#extract what was predicted by weka model
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data << array.concat(pep.aa_counts)
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end
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arff = make_int_arff(Time.now.nsec.to_s,data)
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-
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path = Gem.bin_path('mspire-simulator', 'mspire-simulator').split(/\//)
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dir = path[0..path.size-3].join("/")
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system("java weka.classifiers.trees.M5P -T #{arff} -l #{dir}/lib/weka/M5P.model -p 27 > #{arff}.out")
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system("rm #{arff}")
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#extract what was predicted by weka model
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data/{bin → lib}/weka/M5P.model
RENAMED
File without changes
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File without changes
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data/mspire-simulator.gemspec
CHANGED
@@ -5,14 +5,14 @@
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Gem::Specification.new do |s|
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s.name = "mspire-simulator"
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s.version = "0.1.
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s.version = "0.1.2"
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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 = "2012-08-10"
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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"]
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s.executables = ["mspire-simulator", "sim_mail"]
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s.extra_rdoc_files = [
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"LICENSE.txt",
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"README.rdoc"
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"Rakefile",
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"VERSION",
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"bin/mspire-simulator",
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"bin/sim_mail
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"bin/weka/M5P.model",
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"bin/weka/M5Rules.model",
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"bin/weka/weka.jar",
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"bin/sim_mail",
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"lib/ms/curvefit.rb",
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"lib/ms/curvefit/curve_fit_helper.rb",
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"lib/ms/curvefit/fit_graph.rb",
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"lib/ms/sim_trollop.rb",
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"lib/ms/tr_file_writer.rb",
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"lib/progress.rb",
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"lib/weka/M5P.model",
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"lib/weka/M5Rules.model",
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"mspire-simulator.gemspec",
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"spec/file_writer_spec.rb",
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"spec/merger_spec.rb",
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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: 0.1.
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version: 0.1.2
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prerelease:
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platform: ruby
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authors:
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@@ -177,6 +177,7 @@ description: ! "Simulates MS1 runs given amino acid FASTA files. Outputs an MZML
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email: andrewbnoyce@gmail.com
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executables:
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- mspire-simulator
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- sim_mail
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extensions: []
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extra_rdoc_files:
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- LICENSE.txt
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@@ -187,10 +188,7 @@ files:
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- Rakefile
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- VERSION
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- bin/mspire-simulator
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- bin/sim_mail
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- bin/weka/M5P.model
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- bin/weka/M5Rules.model
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- bin/weka/weka.jar
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- bin/sim_mail
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- lib/ms/curvefit.rb
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- lib/ms/curvefit/curve_fit_helper.rb
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- lib/ms/curvefit/fit_graph.rb
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@@ -209,6 +207,8 @@ files:
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- lib/ms/sim_trollop.rb
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- lib/ms/tr_file_writer.rb
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- lib/progress.rb
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- lib/weka/M5P.model
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- lib/weka/M5Rules.model
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- mspire-simulator.gemspec
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- spec/file_writer_spec.rb
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- spec/merger_spec.rb
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data/bin/weka/weka.jar
DELETED
Binary file
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