mspire 0.6.19 → 0.6.20
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/VERSION +1 -1
- data/lib/ms/fasta.rb +1 -0
- data/lib/ms/mzml/spectrum.rb +5 -0
- data/lib/ms/spectrum.rb +1 -1
- data/spec/ms/mzml_spec.rb +2 -0
- metadata +15 -15
data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.6.
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1
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+
0.6.20
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data/lib/ms/fasta.rb
CHANGED
data/lib/ms/mzml/spectrum.rb
CHANGED
@@ -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'] }
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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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-
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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
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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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1
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: 0.6.
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+
version: 0.6.20
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prerelease:
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platform: ruby
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authors:
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@@ -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: &
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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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- - ~>
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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: *
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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: &
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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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- - ! '>='
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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: *
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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: &
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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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- - ! '>='
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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: *
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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: &
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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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- - ! '>='
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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: *
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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: &
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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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- - ~>
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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: *
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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: &
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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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- - ~>
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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: *
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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: &
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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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- - ! '>='
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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: *
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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
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