mspire-sequest 0.2.6 → 0.2.7

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Files changed (6) hide show
  1. data/History +4 -0
  2. data/README.rdoc +31 -23
  3. data/Rakefile +5 -5
  4. data/VERSION +1 -1
  5. data/spec/mspire/sequest/srf/pepxml_spec.rb +2 -1
  6. metadata +13 -13
data/History CHANGED
@@ -1,3 +1,7 @@
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+ == 0.2.7 / 2011-09-13
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+
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+ Works with mspire libraries. Updated dependencies.
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+
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  == 0.2.0 / 2011-09-13
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  Breaking backwards compatbility. Based on new msplat gem instead of ms-core, ms-ident, etc. MS module instead of Ms module.
data/README.rdoc CHANGED
@@ -1,8 +1,12 @@
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- = ms-sequest
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+ = mspire-sequest
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  An {mspire}[http://mspire.rubyforge.org] library supporting SEQUEST, Bioworks, SQT and associated formats.
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- == {Current API}[http://rubydoc.info/gems/ms-sequest]
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+ == {Current API}[http://rubydoc.info/gems/mspire-sequest]
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+
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+ == Cite
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+
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+ Prince JT, Marcotte EM. <b>mspire: mass spectrometry proteomics in Ruby.</b> *Bioinformatics.* 2008 Dec 1;24(23):2796-7. ({pubmed}[http://www.ncbi.nlm.nih.gov/pubmed/18930952])
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  == Examples
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@@ -10,38 +14,42 @@ Provides two executables for extracting information from an Srf file (run withou
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  srf_to_sqt.rb file.srf # => file.sqt
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  srf_to_search.rb file.srf # => file.mgf (also can make .dta files)
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+ srf_to_pepxml.rb file.srf # => file.xml (pepxml file)
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- === MS::Sequest::Srf
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+ === Mspire::Sequest::Srf
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  Can read and convert Bioworks Sequest Results Files (SRF).
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- require 'ms/sequest/srf'
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- srf = MS::Sequest::Srf.new("file.srf")
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+ require 'mspire/sequest/srf'
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+ srf = Mspire::Sequest::Srf.new("file.srf")
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  Conversions (see api for options):
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- require 'ms/sequest/srf/sqt' # require this in addition to 'ms/sequest/srf'
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+ require 'mspire/sequest/srf/sqt' # require this in addition to 'mspire/sequest/srf'
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  srf.to_sqt # (outputs a file) -> file.sqt
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- require 'ms/sequest/srf/search' # require this in addition to 'ms/sequest/srf'
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+ require 'mspire/sequest/srf/search' # require this in addition to 'mspire/sequest/srf'
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  srf.to_mgf # (outputs a file) -> file.mgf
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  srf.to_dta # (outputs a dir) -> file
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  srf.to_dta("file.tgz", :tgz) # on the fly tgz (requires archive-tar-minitar)
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- Object access (see MS::Sequest::Srf for much more):
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+ require 'mspire/sequest/srf/pepxml' # require this in addition to 'mspire/sequest/srf'
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+ srf.to_pepxml # (outputs a file) -> file.xml
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+
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+ Object access (see Mspire::Sequest::Srf for much more):
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- srf.header # MS::Sequest::Srf::Header object
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- srf.params # MS::Sequest::Params object
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- srf.dta_files # MS::Sequest::Srf::Dta objects
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- srf.out_files # MS::Sequest::Srf::Out objects
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- srf.peptide_hits # MS::Sequest::Srf::Out::Peptide objects
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+ srf.header # Mspire::Sequest::Srf::Header object
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+ srf.params # Mspire::Sequest::Params object
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+ srf.dta_files # Mspire::Sequest::Srf::Dta objects
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+ srf.out_files # Mspire::Sequest::Srf::Out objects
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+ srf.peptide_hits # Mspire::Sequest::Srf::Out::Peptide objects
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- === MS::Sequest::Params
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+ === Mspire::Sequest::Params
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  Object or hash access to any parameter in the file. Also provides a unified interface across several versions (3.1 - 3.3)
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- require 'ms/sequest/params'
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- params = MS::Sequest::Params.new("sequest.params")
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+ require 'mspire/sequest/params'
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+ params = Mspire::Sequest::Params.new("sequest.params")
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  params.any_existing_param # -> some value or empty string if no value
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  params['any_existing_param'] # -> some value or empty string if no value
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  params.non_existent_param # -> nil
@@ -53,13 +61,13 @@ Object or hash access to any parameter in the file. Also provides a unified int
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  params.precursor_mass_type # => "average" | "monoisotopic"
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  params.fragment_mass_type # => "average" | "monoisotopic"
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- === MS::Sequest::Sqt
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+ === Mspire::Sequest::Sqt
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- sqt = MS::Sequest::Sqt.new("file.sqt")
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+ sqt = Mspire::Sequest::Sqt.new("file.sqt")
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  sqt.header
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- sqt.spectra.each do |spectrum| # an MS::Sequest::Sqt::Spectrum object
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- spectrum.matches.each do |match| # an MS::Sequest::Sqt::Match object
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- match.loci.each do |locus| # an MS::Sequest::Sqt::Locus object
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+ sqt.spectra.each do |spectrum| # an Mspire::Sequest::Sqt::Spectrum object
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+ spectrum.matches.each do |match| # an Mspire::Sequest::Sqt::Match object
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+ match.loci.each do |locus| # an Mspire::Sequest::Sqt::Locus object
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  end
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  end
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  end
@@ -69,7 +77,7 @@ Object or hash access to any parameter in the file. Also provides a unified int
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  Also reads Percolator SQT output files intelligently:
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- psqt = MS::Sequest::Sqt.new("percolator_output.sqt")
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+ psqt = Mspire::Sequest::Sqt.new("percolator_output.sqt")
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  psqt.peptide_hits.each do |pmatch|
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  pmatch.percolator_score == pmatch.xcorr
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  pmatch.negative_q_value == pmatch.sp
@@ -78,7 +86,7 @@ Also reads Percolator SQT output files intelligently:
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  == Installation
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- gem install ms-sequest
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+ gem install mspire-sequest
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  == Copyright
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data/Rakefile CHANGED
@@ -11,12 +11,12 @@ Jeweler::Tasks.new do |gem|
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  gem.email = "jtprince@gmail.com"
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  gem.authors = ["John T. Prince"]
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  gem.rubyforge_project = 'mspire'
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- gem.add_runtime_dependency "mspire", "= 0.8.1"
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- gem.add_runtime_dependency "trollop", "~> 1.16"
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- gem.add_development_dependency "jeweler", "~> 1.5.2"
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- gem.add_development_dependency "bio", "~> 1.4.2"
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+ gem.add_runtime_dependency "mspire", "= 0.8.5"
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+ gem.add_runtime_dependency "trollop", "~> 2.0.0"
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+ gem.add_development_dependency "jeweler", "~> 1.8.4"
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+ gem.add_development_dependency "bio", "~> 1.4.3"
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  gem.add_development_dependency "ms-testdata", "= 0.2.1"
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- gem.add_development_dependency "rspec", "~> 2.8.0"
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+ gem.add_development_dependency "rspec", "~> 2.12.0"
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  end
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  Jeweler::RubygemsDotOrgTasks.new
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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.2.6
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+ 0.2.7
data/spec/mspire/sequest/srf/pepxml_spec.rb CHANGED
@@ -57,12 +57,13 @@ describe 'an Mspire::Ident::Pepxml object from an srf file with modifications' d
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  it 'gets everything right' do
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  xml_string = @srf.to_pepxml(:verbose => false).to_xml
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+
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  doc = Nokogiri::XML.parse(xml_string, nil, nil, Nokogiri::XML::ParseOptions::DEFAULT_XML | Nokogiri::XML::ParseOptions::NOBLANKS)
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  root = doc.root
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  root.name.should == "msms_pipeline_analysis"
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- has_attributes( root, 'schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v115.xsd"' )
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+ has_attributes( root, 'xsi:schemaLocation="http://regis-web.systemsbiology.net/pepXML /tools/bin/TPP/tpp/schema/pepXML_v115.xsd"' )
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  root['date'].should_not be_nil
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  root['summary_xml'].should match( "020.xml" )
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  root.namespaces.should == ( {"xmlns" => "http://regis-web.systemsbiology.net/pepXML" } )
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: mspire-sequest
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  version: !ruby/object:Gem::Version
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- version: 0.2.6
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+ version: 0.2.7
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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: 2012-07-25 00:00:00.000000000 Z
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+ date: 2012-12-18 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: 0.8.1
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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: 0.8.1
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+ version: 0.8.5
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  - !ruby/object:Gem::Dependency
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  name: trollop
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  requirement: !ruby/object:Gem::Requirement
@@ -34,7 +34,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '1.16'
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+ version: 2.0.0
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  type: :runtime
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -42,7 +42,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: '1.16'
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+ version: 2.0.0
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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  requirement: !ruby/object:Gem::Requirement
@@ -50,7 +50,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 1.5.2
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+ version: 1.8.4
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -58,7 +58,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 1.5.2
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+ version: 1.8.4
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  - !ruby/object:Gem::Dependency
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  name: bio
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  requirement: !ruby/object:Gem::Requirement
@@ -66,7 +66,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 1.4.2
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+ version: 1.4.3
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -74,7 +74,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 1.4.2
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+ version: 1.4.3
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  - !ruby/object:Gem::Dependency
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  name: ms-testdata
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  requirement: !ruby/object:Gem::Requirement
@@ -98,7 +98,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 2.8.0
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+ version: 2.12.0
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  type: :development
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  prerelease: false
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  version_requirements: !ruby/object:Gem::Requirement
@@ -106,7 +106,7 @@ dependencies:
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  requirements:
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  - - ~>
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  - !ruby/object:Gem::Version
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- version: 2.8.0
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+ version: 2.12.0
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  description: reads .SRF, .SQT and supports conversions
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  email: jtprince@gmail.com
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  executables:
@@ -178,7 +178,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project: mspire
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- rubygems_version: 1.8.24
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+ rubygems_version: 1.8.23
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  signing_key:
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  specification_version: 3
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  summary: An mspire library supporting SEQUEST, Bioworks, SQT, etc