mzml 0.1.0

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Files changed (16) hide show
  1. data/.document +5 -0
  2. data/.gitignore +22 -0
  3. data/.yardoc +0 -0
  4. data/LICENSE +20 -0
  5. data/README.rdoc +20 -0
  6. data/Rakefile +44 -0
  7. data/VERSION +1 -0
  8. data/lib/mzml.rb +228 -0
  9. data/mzml.gemspec +62 -0
  10. data/spec/mzml_spec.rb +60 -0
  11. data/spec/small.compressed.mzML +11416 -0
  12. data/spec/small.mgf +350 -0
  13. data/spec/small.mzML +11405 -0
  14. data/spec/spec.opts +1 -0
  15. data/spec/spec_helper.rb +27 -0
  16. metadata +90 -0
data/spec/spec.opts ADDED
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+ --color
data/spec/spec_helper.rb ADDED
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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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+ require 'rubygems'
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+ require 'mzml'
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+ require 'spec'
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+ require 'spec/autorun'
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+
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+ class Mgf < Struct.new(:title, :mz, :intensity); end
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+
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+ def parse_mgf(fname)
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+ mgf = Mgf.new(nil,[],[])
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+ File.open(fname).each do |l|
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+ l.chomp!
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+ case l
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+ when /^TITLE=(.+)/
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+ mgf.title = $1
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+ when /^\d/
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+ m,i = l.split().map{|e| (e.to_f * 1000).to_i() / 1000.0 }
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+ mgf.mz << m
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+ mgf.intensity << i
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+ end
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+ end
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+ return mgf
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+ end
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+
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+ Spec::Runner.configure do |config|
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: mzml
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+ version: !ruby/object:Gem::Version
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+ version: 0.1.0
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+ platform: ruby
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+ authors:
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+ - Angel Pizarro
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+
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+ date: 2009-12-06 00:00:00 +00:00
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+ default_executable:
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: rspec
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+ type: :development
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+ version_requirement:
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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: 1.2.9
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+ version:
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+ - !ruby/object:Gem::Dependency
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+ name: nokogiri
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+ type: :runtime
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+ version_requirement:
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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: 1.3.3
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+ version:
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+ description: A non-validating mzML parser. MzML is a standard data format for representing mass spectrometry data.
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+ email: angel@delagoya.com
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+ executables: []
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+
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+ extensions: []
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+
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+ extra_rdoc_files:
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+ - LICENSE
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+ - README.rdoc
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+ files:
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+ - .document
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+ - .gitignore
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+ - .yardoc
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+ - LICENSE
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+ - README.rdoc
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+ - Rakefile
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+ - VERSION
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+ - lib/mzml.rb
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+ - mzml.gemspec
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+ - spec/mzml_spec.rb
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+ - spec/small.compressed.mzML
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+ - spec/small.mgf
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+ - spec/small.mzML
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+ - spec/spec.opts
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+ - spec/spec_helper.rb
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+ has_rdoc: true
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+ homepage: http://github.com/delagoya/mzml
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+ licenses: []
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+
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+ post_install_message:
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+ rdoc_options:
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+ - --charset=UTF-8
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+ require_paths:
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+ - lib
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+ required_ruby_version: !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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+ version:
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+ required_rubygems_version: !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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+ version:
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+ requirements: []
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+
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+ rubyforge_project:
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+ rubygems_version: 1.3.5
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+ signing_key:
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+ specification_version: 3
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+ summary: A non-validating mzML parser
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+ test_files:
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+ - spec/mzml_spec.rb
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+ - spec/spec_helper.rb