mspire 0.8.6.2 → 0.8.7

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.
@@ -102,9 +102,7 @@ end
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  to_run.each do |file_base, bundle|
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  putsv "calculating qvalues for #{file_base}"
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  hit_and_qvalue_pairs = Mspire::ErrorRate::Qvalue.target_decoy_qvalues(bundle.target, bundle.decoy, :z_together => opt[:z_together])
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-
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  outfile = Mspire::Ident::PeptideHit::Qvalue.to_phq(file_base, *hit_and_qvalue_pairs.transpose)
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-
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  putsv "created: #{outfile}"
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  end
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data/spec/spec_helper.rb CHANGED
@@ -1,8 +1,11 @@
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- $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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- $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ #$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ #$LOAD_PATH.unshift(File.dirname(__FILE__))
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+
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+ require 'simplecov'
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+ SimpleCov.start
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- require 'rubygems'
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  require 'rspec'
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+ require 'spec_utilities'
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  TESTFILES = File.dirname(__FILE__) + '/testfiles'
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@@ -19,47 +22,3 @@ RSpec.configure do |config|
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  end
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- def benchmark(*args, &block)
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- if ENV['BENCHMARK']
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- Benchmark.bmbm(*args, &block)
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- end
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- end
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-
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- # given "filename.ext" returns "filename.CHECK.ext
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- # block can be given to sanitize each string
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- def file_check(filename, delete=true, &block)
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- ext = File.extname(filename)
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- base = filename.chomp(ext)
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- checkfile = base + ".CHECK" + ext
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- File.exist?(filename).should be_true
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- fstring = IO.read(filename)
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- cstring = IO.read(checkfile)
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- if block
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- (fstring, cstring) = [fstring, cstring].map do |string|
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- block.call(string)
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- end
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- end
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- fstring.should == cstring
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- File.unlink(filename) if delete
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- end
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-
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- def sanitize_mspire_version_xml(string)
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- string.gsub(/"mspire(_[\d\.]+)?" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
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- .gsub(/softwareRef="mspire_[\d\.]+/, 'softwareRef="mspire_X.X.X')
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- end
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-
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- require 'stringio'
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-
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- module Kernel
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-
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- def capture_stdout
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- out = StringIO.new
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- $stdout = out
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- yield
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- out.string
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- ensure
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- $stdout = STDOUT
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- end
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-
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- end
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-
@@ -0,0 +1,45 @@
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+
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+ def benchmark(*args, &block)
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+ if ENV['BENCHMARK']
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+ Benchmark.bmbm(*args, &block)
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+ end
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+ end
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+
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+ # given "filename.ext" returns "filename.CHECK.ext
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+ # block can be given to sanitize each string
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+ def file_check(filename, delete=true, &block)
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+ ext = File.extname(filename)
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+ base = filename.chomp(ext)
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+ checkfile = base + ".CHECK" + ext
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+ File.exist?(filename).should be_true
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+ fstring = IO.read(filename)
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+ cstring = IO.read(checkfile)
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+ if block
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+ (fstring, cstring) = [fstring, cstring].map do |string|
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+ block.call(string)
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+ end
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+ end
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+ fstring.should == cstring
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+ File.unlink(filename) if delete
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+ end
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+
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+ def sanitize_mspire_version_xml(string)
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+ string.gsub(/"mspire(_[\d\.]+)?" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})
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+ .gsub(/softwareRef="mspire_[\d\.]+/, 'softwareRef="mspire_X.X.X')
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+ end
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+
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+ require 'stringio'
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+
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+ module Kernel
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+
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+ def capture_stdout
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+ out = StringIO.new
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+ $stdout = out
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+ yield
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+ out.string
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+ ensure
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+ $stdout = STDOUT
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+ end
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+
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+ end
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+
metadata CHANGED
@@ -1,8 +1,7 @@
1
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  --- !ruby/object:Gem::Specification
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  name: mspire
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  version: !ruby/object:Gem::Version
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- version: 0.8.6.2
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- prerelease:
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+ version: 0.8.7
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  platform: ruby
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  authors:
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  - John T. Prince
@@ -10,12 +9,11 @@ authors:
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-05-29 00:00:00.000000000 Z
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+ date: 2013-07-31 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: nokogiri
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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
@@ -23,7 +21,6 @@ dependencies:
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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
@@ -31,55 +28,48 @@ dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bsearch
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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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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: 1.5.0
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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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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: 1.5.0
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  - !ruby/object:Gem::Dependency
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  name: andand
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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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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: 1.3.3
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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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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: 1.3.3
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  - !ruby/object:Gem::Dependency
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  name: obo
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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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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: 0.1.3
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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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+ - - '>='
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  - !ruby/object:Gem::Version
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  version: 0.1.3
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  - !ruby/object:Gem::Dependency
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  name: builder
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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
@@ -87,7 +77,6 @@ dependencies:
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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
@@ -95,7 +84,6 @@ dependencies:
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  - !ruby/object:Gem::Dependency
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  name: bio
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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
@@ -103,7 +91,6 @@ dependencies:
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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
@@ -111,7 +98,6 @@ dependencies:
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  - !ruby/object:Gem::Dependency
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  name: trollop
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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
@@ -119,73 +105,123 @@ dependencies:
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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: 2.0.0
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  - !ruby/object:Gem::Dependency
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- name: fftw3
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+ name: bundler
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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: '0.3'
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+ version: '1.3'
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  type: :development
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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: '0.3'
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+ version: '1.3'
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+ - !ruby/object:Gem::Dependency
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+ name: rake
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  - !ruby/object:Gem::Dependency
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  name: rspec
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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: '2.13'
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+ version: 2.13.0
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  type: :development
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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: '2.13'
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+ version: 2.13.0
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  - !ruby/object:Gem::Dependency
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- name: jeweler
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+ name: rdoc
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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: 1.8.4
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+ version: '3.12'
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  type: :development
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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: 1.8.4
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+ version: '3.12'
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+ - !ruby/object:Gem::Dependency
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+ name: simplecov
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: coveralls
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: fftw3
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '0.3'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
207
+ - - ~>
208
+ - !ruby/object:Gem::Version
209
+ version: '0.3'
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  description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
176
211
  merging of ms-* gems
177
- email: jtprince@gmail.com
212
+ email:
213
+ - jtprince@gmail.com
178
214
  executables:
179
215
  - mspire
180
216
  extensions: []
181
- extra_rdoc_files:
182
- - LICENSE
183
- - README.md
217
+ extra_rdoc_files: []
184
218
  files:
219
+ - .gitignore
220
+ - .travis.yml
221
+ - Gemfile
185
222
  - LICENSE
186
223
  - README.md
187
224
  - Rakefile
188
- - VERSION
189
225
  - bin/mspire
190
226
  - lib/core_ext/array/in_groups.rb
191
227
  - lib/core_ext/enumerable.rb
@@ -288,6 +324,7 @@ files:
288
324
  - lib/mspire/spectrum_like.rb
289
325
  - lib/mspire/tagged_peak.rb
290
326
  - lib/mspire/user_param.rb
327
+ - lib/mspire/version.rb
291
328
  - lib/obo/ims.rb
292
329
  - lib/obo/ms.rb
293
330
  - lib/obo/ontology.rb
@@ -295,6 +332,7 @@ files:
295
332
  - lib/openany.rb
296
333
  - lib/write_file_or_string.rb
297
334
  - obo/ims.obo
335
+ - obo/mod.obo
298
336
  - obo/ms.obo
299
337
  - obo/unit.obo
300
338
  - schema/peptide_hit_qvalues.pqh.tsv
@@ -348,6 +386,7 @@ files:
348
386
  - spec/mspire_spec.rb
349
387
  - spec/obo_spec.rb
350
388
  - spec/spec_helper.rb
389
+ - spec/spec_utilities.rb
351
390
  - spec/testfiles/continuous_binary.tmp.ibd
352
391
  - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.PEPTIDE_CENTRIC.yml
353
392
  - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
@@ -386,26 +425,101 @@ files:
386
425
  homepage: http://github.com/princelab/mspire
387
426
  licenses:
388
427
  - MIT
428
+ metadata: {}
389
429
  post_install_message:
390
430
  rdoc_options: []
391
431
  require_paths:
392
432
  - lib
393
433
  required_ruby_version: !ruby/object:Gem::Requirement
394
- none: false
395
434
  requirements:
396
- - - ! '>='
435
+ - - '>='
397
436
  - !ruby/object:Gem::Version
398
437
  version: '0'
399
438
  required_rubygems_version: !ruby/object:Gem::Requirement
400
- none: false
401
439
  requirements:
402
- - - ! '>='
440
+ - - '>='
403
441
  - !ruby/object:Gem::Version
404
442
  version: '0'
405
443
  requirements: []
406
444
  rubyforge_project:
407
- rubygems_version: 1.8.23
445
+ rubygems_version: 2.0.3
408
446
  signing_key:
409
- specification_version: 3
447
+ specification_version: 4
410
448
  summary: mass spectrometry proteomics, lipidomics, and tools
411
- test_files: []
449
+ test_files:
450
+ - spec/cv/param_spec.rb
451
+ - spec/mspire/bin_spec.rb
452
+ - spec/mspire/cv/obo_spec.rb
453
+ - spec/mspire/cv/param_spec.rb
454
+ - spec/mspire/cv/paramable_spec.rb
455
+ - spec/mspire/digester_spec.rb
456
+ - spec/mspire/error_rate/qvalue_spec.rb
457
+ - spec/mspire/fasta_spec.rb
458
+ - spec/mspire/ident/peptide/db/creator_spec.rb
459
+ - spec/mspire/ident/peptide/db/io_spec.rb
460
+ - spec/mspire/ident/peptide/db_spec.rb
461
+ - spec/mspire/ident/pepxml/sample_enzyme_spec.rb
462
+ - spec/mspire/ident/pepxml/search_hit/modification_info_spec.rb
463
+ - spec/mspire/ident/pepxml_spec.rb
464
+ - spec/mspire/ident/protein_group_spec.rb
465
+ - spec/mspire/imzml/writer_spec.rb
466
+ - spec/mspire/isotope/aa_spec.rb
467
+ - spec/mspire/isotope/distribution_spec.rb
468
+ - spec/mspire/isotope_spec.rb
469
+ - spec/mspire/mass_spec.rb
470
+ - spec/mspire/molecular_formula_spec.rb
471
+ - spec/mspire/mzml/cv_spec.rb
472
+ - spec/mspire/mzml/data_array_spec.rb
473
+ - spec/mspire/mzml/file_content_spec.rb
474
+ - spec/mspire/mzml/index_list_spec.rb
475
+ - spec/mspire/mzml/plms1_spec.rb
476
+ - spec/mspire/mzml/referenceable_param_group_spec.rb
477
+ - spec/mspire/mzml/source_file_spec.rb
478
+ - spec/mspire/mzml/spectrum_list_spec.rb
479
+ - spec/mspire/mzml/spectrum_spec.rb
480
+ - spec/mspire/mzml_spec.rb
481
+ - spec/mspire/peaklist_spec.rb
482
+ - spec/mspire/plms1_spec.rb
483
+ - spec/mspire/quant/qspec_spec.rb
484
+ - spec/mspire/readme_spec.rb
485
+ - spec/mspire/spectrum_spec.rb
486
+ - spec/mspire/user_param_spec.rb
487
+ - spec/mspire_spec.rb
488
+ - spec/obo_spec.rb
489
+ - spec/spec_helper.rb
490
+ - spec/spec_utilities.rb
491
+ - spec/testfiles/continuous_binary.tmp.ibd
492
+ - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.PEPTIDE_CENTRIC.yml
493
+ - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.fasta
494
+ - spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
495
+ - spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.ibd
496
+ - spec/testfiles/mspire/imzml/1_BB7_SIM_478.5.CHECK.imzML
497
+ - spec/testfiles/mspire/imzml/continuous_binary.CHECK.ibd
498
+ - spec/testfiles/mspire/imzml/processed_binary.CHECK.ibd
499
+ - spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.mzML
500
+ - spec/testfiles/mspire/mzml/j24z.idx_comp.3.NORMALIZED.CHECK.mzML
501
+ - spec/testfiles/mspire/mzml/j24z.idx_comp.3.ROUNDTRIP.CHECK.mzML
502
+ - spec/testfiles/mspire/mzml/j24z.idx_comp.3.mzML
503
+ - spec/testfiles/mspire/mzml/mspire_simulated.MSn.CHECK.mzML
504
+ - spec/testfiles/mspire/mzml/openms.noidx_nocomp.12.mzML
505
+ - spec/testfiles/mspire/quant/kill_extra_tabs.rb
506
+ - spec/testfiles/mspire/quant/max_quant_output.provenance.txt
507
+ - spec/testfiles/mspire/quant/max_quant_output.txt
508
+ - spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv
509
+ - spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp
510
+ - spec/testfiles/mspire/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv
511
+ - spec/testfiles/mspire/quant/pdcd5_final.txt
512
+ - spec/testfiles/mspire/quant/pdcd5_final.txt_qspecgp
513
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.CSV.csv
514
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.csv
515
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.csv
516
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv
517
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp
518
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv
519
+ - spec/testfiles/mspire/quant/pdcd5_lfq_qspec.txt
520
+ - spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt
521
+ - spec/testfiles/mspire/quant/pdcd5_lfq_tabdel.txt_qspecgp
522
+ - spec/testfiles/mspire/quant/remove_rest_of_proteins.rb
523
+ - spec/testfiles/mspire/quant/unlog_transform.rb
524
+ - spec/testfiles/plms1/output.key
525
+ - spec/testfiles/processed_binary.tmp.ibd
data/VERSION DELETED
@@ -1 +0,0 @@
1
- 0.8.6.2