mspire 0.6.19 → 0.6.20

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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.6.19
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+ 0.6.20
data/lib/ms/fasta.rb CHANGED
@@ -45,6 +45,7 @@ module MS
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  # yields each Bio::FastaFormat object in turn
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  def self.foreach(file, &block)
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+ block or return enum_for(__method__, file)
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  Bio::FlatFile.open(Bio::FastaFormat, file) do |fasta|
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  fasta.each(&block)
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  end
@@ -73,7 +73,12 @@ module MS
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  params[cvparam[:accession]] = cvparam[:value]
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  end
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  spec.ms_level = params['MS:1000511'].to_i
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+ # we assume centroid if they don't tell us profile
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+ spec.centroided = !params.key?("MS:1000128") # profile spectrum
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+ # centroid -> "MS:1000127"
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+
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  # TODO: need to slot in all the other info in reasonable ways
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+ # TODO: need to make sure we deal with referencable params
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  data_arrays = xml.xpath('./binaryDataArrayList/binaryDataArray').map do |binary_data_array_n|
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  accessions = binary_data_array_n.xpath('./cvParam').map {|node| node['accession'] }
data/lib/ms/spectrum.rb CHANGED
@@ -52,7 +52,7 @@ module MS
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  def merge(spectra, opts={})
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  opt = DEFAULT_MERGE.merge(opts)
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  (spectrum, returned_data) =
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- if spectra.first.centroided?
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+ unless spectra.first.centroided? == false
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  # find the min and max across all spectra
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  first_mzs = spectra.first.mzs
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  min = first_mzs.first ; max = first_mzs.last
data/spec/ms/mzml_spec.rb CHANGED
@@ -40,8 +40,10 @@ describe MS::Mzml do
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  it 'goes through spectrum with #each or #each_spectrum' do
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  mz_sizes = [20168, 315, 634]
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+ centroided = [false, true, true]
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  @mzml.each do |spec|
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  spec.mzs.size.should == mz_sizes.shift
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+ spec.centroided?.should == centroided.shift
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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
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  version: !ruby/object:Gem::Version
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- version: 0.6.19
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+ version: 0.6.20
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  prerelease:
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  platform: ruby
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  authors:
@@ -14,7 +14,7 @@ date: 2012-02-24 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: &10271800 !ruby/object:Gem::Requirement
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+ requirement: &23959880 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -22,10 +22,10 @@ dependencies:
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  version: '1.5'
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  type: :runtime
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  prerelease: false
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- version_requirements: *10271800
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+ version_requirements: *23959880
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  - !ruby/object:Gem::Dependency
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  name: bsearch
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- requirement: &10656900 !ruby/object:Gem::Requirement
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+ requirement: &23959360 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
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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: *10656900
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+ version_requirements: *23959360
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  - !ruby/object:Gem::Dependency
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  name: andand
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- requirement: &10739280 !ruby/object:Gem::Requirement
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+ requirement: &23958860 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
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  version: 1.3.1
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  type: :runtime
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  prerelease: false
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- version_requirements: *10739280
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+ version_requirements: *23958860
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  - !ruby/object:Gem::Dependency
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  name: obo
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- requirement: &10814460 !ruby/object:Gem::Requirement
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+ requirement: &23958340 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
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  version: 0.1.0
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  type: :runtime
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  prerelease: false
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- version_requirements: *10814460
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+ version_requirements: *23958340
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  - !ruby/object:Gem::Dependency
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  name: rspec
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- requirement: &10811160 !ruby/object:Gem::Requirement
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+ requirement: &23974240 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -66,10 +66,10 @@ dependencies:
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  version: '2.6'
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  type: :development
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  prerelease: false
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- version_requirements: *10811160
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+ version_requirements: *23974240
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &10888880 !ruby/object:Gem::Requirement
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+ requirement: &23973760 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -77,10 +77,10 @@ dependencies:
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  version: 1.5.2
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  type: :development
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  prerelease: false
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- version_requirements: *10888880
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+ version_requirements: *23973760
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  - !ruby/object:Gem::Dependency
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  name: rcov
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- requirement: &10902860 !ruby/object:Gem::Requirement
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+ requirement: &23973280 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *10902860
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+ version_requirements: *23973280
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  description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
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  merging of ms-* gems
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  email: jtprince@gmail.com