mspire 0.8.0 → 0.8.1
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/README.md +60 -0
- data/Rakefile +16 -4
- data/VERSION +1 -1
- data/lib/mspire/imzml/writer/commandline.rb +1 -1
- data/lib/mspire/imzml/writer.rb +20 -1
- data/lib/mspire/mzml/cv.rb +3 -4
- data/obo/ims.obo +2 -4
- data/obo/ms.obo +708 -56
- data/obo/unit.obo +1 -1
- data/spec/mspire/imzml/writer_spec.rb +30 -0
- data/spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.CHECK.ibd +0 -0
- data/spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.CHECK.imzML +3975 -0
- data/spec/testfiles/mspire/mzml/mspire_simulated.MSn.check.mzML +2 -2
- metadata +6 -4
- data/README.rdoc +0 -24
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<?xml version="1.0" encoding="UTF-8"?>
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<mzML xmlns="http://psi.hupo.org/ms/mzml" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" version="1.1.0" id="ms1_and_ms2">
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<cvList count="3">
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<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.
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<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" version="
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<cv id="MS" fullName="Proteomics Standards Initiative Mass Spectrometry Ontology" URI="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo" version="3.29.0"/>
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<cv id="UO" fullName="Unit Ontology" URI="http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo" version="12:10:2011"/>
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<cv id="IMS" fullName="Imaging MS Ontology" URI="http://www.maldi-msi.org/download/imzml/imagingMS.obo" version="0.9.1"/>
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</cvList>
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<fileDescription>
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metadata
CHANGED
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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.
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version: 0.8.1
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prerelease:
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platform: ruby
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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-
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date: 2012-07-25 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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@@ -196,10 +196,10 @@ executables:
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extensions: []
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extra_rdoc_files:
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- LICENSE
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- README.
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- README.md
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files:
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- LICENSE
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- README.
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- README.md
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- Rakefile
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- VERSION
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- bin/mspire
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- spec/testfiles/mspire/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml
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- spec/testfiles/mspire/imzml/continuous_binary_check.ibd
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- spec/testfiles/mspire/imzml/processed_binary_check.ibd
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- spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.CHECK.ibd
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- spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.CHECK.imzML
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- spec/testfiles/mspire/mzml/1_BB7_SIM_478.5.mzML
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- spec/testfiles/mspire/mzml/j24z.idx_comp.3.mzML
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- spec/testfiles/mspire/mzml/mspire_simulated.MSn.check.mzML
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data/README.rdoc
DELETED
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= mspire
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Tools for working with mass spectrometry data in ruby.
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== Examples
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=== mzml
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require 'ms/mzml'
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MS::Mzml.open("somefile.mzml") do |mzml|
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spectrum = mzml[0] # the first spectrum ( same as mzml.spectrum(0) )
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spectrum = mzml["controllerType=0 controllerNumber=1 scan=2"] # query by id string
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mzml.spectrum_from_scan_num(23) # raises ScanNumbersNotFound or ScanNumbersNotUnique errors if problems
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end
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require 'ms/mass/aa'
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MS::Mass::AA::MONO['A'] # or access by symbol
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== Copyright
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See LICENSE (MIT)
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