mspire 0.6.20 → 0.6.21

data/VERSION

@@ -1 +1 @@
-0.6.20
+0.6.21

data/lib/ms/mzml/precursor.rb

@@ -1,4 +1,5 @@
 require 'ms/mzml/list'
+require 'ms/mzml/selected_ion'
 
 module MS
   class Mzml
@@ -20,6 +21,10 @@ module MS
       # a boolean indicating the spectrum is from an external source file
       attr_accessor :from_external_source_file
 
+      def initialize(spectrum_derived_from=nil)
+        @spectrum=spectrum_derived_from
+      end
+
       def to_xml(builder)
         atts = {}
         if @from_external_source_file
@@ -30,8 +35,8 @@ module MS
         end
         builder.precursor(atts) do |prec_n|
           @isolation_window.to_xml(prec_n) if @isolation_window
-          MS::Mzml::SelectedIonList.list_xml(@selected_ions, prec_n) if @selected_ions
-          @activation.to_xml(prec_n)
+          MS::Mzml::SelectedIon.list_xml(@selected_ions, prec_n) if @selected_ions
+          @activation.to_xml(prec_n) if @activation
         end
       end
 

data/lib/ms/mzml.rb

@@ -8,6 +8,7 @@ require 'ms/mzml/spectrum'
 require 'ms/mzml/file_description'
 require 'ms/mzml/software'
 require 'ms/mzml/scan_list'
+require 'ms/mzml/selected_ion'
 require 'ms/mzml/scan'
 require 'ms/mzml/scan_settings'
 require 'ms/mzml/processing_method'

data/mspire.gemspec

@@ -0,0 +1,200 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "mspire"
+  s.version = "0.6.20"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["John T. Prince", "Simon Chiang"]
+  s.date = "2012-02-24"
+  s.description = "mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire, merging of ms-* gems"
+  s.email = "jtprince@gmail.com"
+  s.extra_rdoc_files = [
+    "LICENSE",
+    "README.rdoc"
+  ]
+  s.files = [
+    "LICENSE",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "lib/bin.rb",
+    "lib/core_ext/array/in_groups.rb",
+    "lib/cv.rb",
+    "lib/cv/param.rb",
+    "lib/cv/referenceable_param_group_ref.rb",
+    "lib/io/bookmark.rb",
+    "lib/merge.rb",
+    "lib/ms.rb",
+    "lib/ms/cv.rb",
+    "lib/ms/cv/param.rb",
+    "lib/ms/cv/paramable.rb",
+    "lib/ms/digester.rb",
+    "lib/ms/fasta.rb",
+    "lib/ms/ident.rb",
+    "lib/ms/ident/peptide.rb",
+    "lib/ms/ident/peptide/db.rb",
+    "lib/ms/ident/peptide_hit.rb",
+    "lib/ms/ident/peptide_hit/qvalue.rb",
+    "lib/ms/ident/pepxml.rb",
+    "lib/ms/ident/pepxml/modifications.rb",
+    "lib/ms/ident/pepxml/msms_pipeline_analysis.rb",
+    "lib/ms/ident/pepxml/msms_run_summary.rb",
+    "lib/ms/ident/pepxml/parameters.rb",
+    "lib/ms/ident/pepxml/sample_enzyme.rb",
+    "lib/ms/ident/pepxml/search_database.rb",
+    "lib/ms/ident/pepxml/search_hit.rb",
+    "lib/ms/ident/pepxml/search_hit/modification_info.rb",
+    "lib/ms/ident/pepxml/search_result.rb",
+    "lib/ms/ident/pepxml/search_summary.rb",
+    "lib/ms/ident/pepxml/spectrum_query.rb",
+    "lib/ms/ident/protein.rb",
+    "lib/ms/ident/protein_group.rb",
+    "lib/ms/ident/search.rb",
+    "lib/ms/isotope/aa.rb",
+    "lib/ms/mascot.rb",
+    "lib/ms/mass.rb",
+    "lib/ms/mass/aa.rb",
+    "lib/ms/mzml.rb",
+    "lib/ms/mzml/activation.rb",
+    "lib/ms/mzml/chromatogram.rb",
+    "lib/ms/mzml/chromatogram_list.rb",
+    "lib/ms/mzml/component.rb",
+    "lib/ms/mzml/contact.rb",
+    "lib/ms/mzml/cv.rb",
+    "lib/ms/mzml/data_array.rb",
+    "lib/ms/mzml/data_array_container_like.rb",
+    "lib/ms/mzml/data_processing.rb",
+    "lib/ms/mzml/file_content.rb",
+    "lib/ms/mzml/file_description.rb",
+    "lib/ms/mzml/index_list.rb",
+    "lib/ms/mzml/instrument_configuration.rb",
+    "lib/ms/mzml/isolation_window.rb",
+    "lib/ms/mzml/list.rb",
+    "lib/ms/mzml/plms1.rb",
+    "lib/ms/mzml/precursor.rb",
+    "lib/ms/mzml/processing_method.rb",
+    "lib/ms/mzml/product.rb",
+    "lib/ms/mzml/referenceable_param_group.rb",
+    "lib/ms/mzml/run.rb",
+    "lib/ms/mzml/sample.rb",
+    "lib/ms/mzml/scan.rb",
+    "lib/ms/mzml/scan_list.rb",
+    "lib/ms/mzml/scan_settings.rb",
+    "lib/ms/mzml/selected_ion.rb",
+    "lib/ms/mzml/software.rb",
+    "lib/ms/mzml/source_file.rb",
+    "lib/ms/mzml/spectrum.rb",
+    "lib/ms/mzml/spectrum_list.rb",
+    "lib/ms/obo.rb",
+    "lib/ms/peak.rb",
+    "lib/ms/peak/point.rb",
+    "lib/ms/plms1.rb",
+    "lib/ms/quant/qspec.rb",
+    "lib/ms/quant/qspec/protein_group_comparison.rb",
+    "lib/ms/spectrum.rb",
+    "lib/ms/spectrum/centroid.rb",
+    "lib/ms/spectrum_like.rb",
+    "lib/ms/user_param.rb",
+    "lib/mspire.rb",
+    "lib/obo/ims.rb",
+    "lib/obo/ms.rb",
+    "lib/obo/ontology.rb",
+    "lib/obo/unit.rb",
+    "lib/openany.rb",
+    "lib/write_file_or_string.rb",
+    "obo/ims.obo",
+    "obo/ms.obo",
+    "obo/unit.obo",
+    "spec/bin_spec.rb",
+    "spec/ms/cv/param_spec.rb",
+    "spec/ms/digester_spec.rb",
+    "spec/ms/fasta_spec.rb",
+    "spec/ms/ident/peptide/db_spec.rb",
+    "spec/ms/ident/pepxml/sample_enzyme_spec.rb",
+    "spec/ms/ident/pepxml/search_hit/modification_info_spec.rb",
+    "spec/ms/ident/pepxml_spec.rb",
+    "spec/ms/ident/protein_group_spec.rb",
+    "spec/ms/isotope/aa_spec.rb",
+    "spec/ms/mass_spec.rb",
+    "spec/ms/mzml/cv_spec.rb",
+    "spec/ms/mzml/file_content_spec.rb",
+    "spec/ms/mzml/file_description_spec.rb",
+    "spec/ms/mzml/index_list_spec.rb",
+    "spec/ms/mzml/plms1_spec.rb",
+    "spec/ms/mzml/referenceable_param_group_spec.rb",
+    "spec/ms/mzml_spec.rb",
+    "spec/ms/peak_spec.rb",
+    "spec/ms/plms1_spec.rb",
+    "spec/ms/quant/qspec_spec.rb",
+    "spec/ms/spectrum_spec.rb",
+    "spec/ms/user_param_spec.rb",
+    "spec/mspire_spec.rb",
+    "spec/obo_spec.rb",
+    "spec/spec_helper.rb",
+    "spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.fasta",
+    "spec/testfiles/ms/ident/peptide/db/uni_11_sp_tr.msd_clvg2.min_aaseq4.yml",
+    "spec/testfiles/ms/mzml/j24z.idx_comp.3.mzML",
+    "spec/testfiles/ms/mzml/mspire_simulated.noidx.check.mzML",
+    "spec/testfiles/ms/mzml/openms.noidx_nocomp.12.mzML",
+    "spec/testfiles/ms/quant/kill_extra_tabs.rb",
+    "spec/testfiles/ms/quant/max_quant_output.provenance.txt",
+    "spec/testfiles/ms/quant/max_quant_output.txt",
+    "spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv",
+    "spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp",
+    "spec/testfiles/ms/quant/pdcd5_final.killedextratabs.tsv_qspecgp.csv",
+    "spec/testfiles/ms/quant/pdcd5_final.txt",
+    "spec/testfiles/ms/quant/pdcd5_final.txt_qspecgp",
+    "spec/testfiles/ms/quant/pdcd5_lfq_qspec.CSV.csv",
+    "spec/testfiles/ms/quant/pdcd5_lfq_qspec.csv",
+    "spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.csv",
+    "spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv",
+    "spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp",
+    "spec/testfiles/ms/quant/pdcd5_lfq_qspec.oneprot.tsv_qspecgp.csv",
+    "spec/testfiles/ms/quant/pdcd5_lfq_qspec.txt",
+    "spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt",
+    "spec/testfiles/ms/quant/pdcd5_lfq_tabdel.txt_qspecgp",
+    "spec/testfiles/ms/quant/remove_rest_of_proteins.rb",
+    "spec/testfiles/ms/quant/unlog_transform.rb",
+    "spec/testfiles/plms1/output.key"
+  ]
+  s.homepage = "http://github.com/princelab/mspire"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "1.8.15"
+  s.summary = "mass spectrometry proteomics, lipidomics, and tools"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<nokogiri>, ["~> 1.5"])
+      s.add_runtime_dependency(%q<bsearch>, [">= 1.5.0"])
+      s.add_runtime_dependency(%q<andand>, [">= 1.3.1"])
+      s.add_runtime_dependency(%q<obo>, [">= 0.1.0"])
+      s.add_development_dependency(%q<rspec>, ["~> 2.6"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_development_dependency(%q<rcov>, [">= 0"])
+    else
+      s.add_dependency(%q<nokogiri>, ["~> 1.5"])
+      s.add_dependency(%q<bsearch>, [">= 1.5.0"])
+      s.add_dependency(%q<andand>, [">= 1.3.1"])
+      s.add_dependency(%q<obo>, [">= 0.1.0"])
+      s.add_dependency(%q<rspec>, ["~> 2.6"])
+      s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+      s.add_dependency(%q<rcov>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<nokogiri>, ["~> 1.5"])
+    s.add_dependency(%q<bsearch>, [">= 1.5.0"])
+    s.add_dependency(%q<andand>, [">= 1.3.1"])
+    s.add_dependency(%q<obo>, [">= 0.1.0"])
+    s.add_dependency(%q<rspec>, ["~> 2.6"])
+    s.add_dependency(%q<jeweler>, ["~> 1.5.2"])
+    s.add_dependency(%q<rcov>, [">= 0"])
+  end
+end
+

data/spec/ms/fasta_spec.rb

@@ -77,6 +77,12 @@ describe 'basic fasta operations' do
     end
   end
 
+  it 'gives an iterator called with MS::Fasta.foreach and no block' do
+    seqs = MS::Fasta.foreach(@data['newlines_file']).select {|e| e.header =~ /^gi/ }.map(&:sequence)
+    seqs.size.should == 1
+    seqs.first[0,4].should == 'LCLY'
+  end
+
   it 'runs the documentation' do
     fasta_file = @data['newlines_file']
     ids = MS::Fasta.open(fasta_file) do |fasta| 

data/spec/ms/mzml_spec.rb

@@ -76,6 +76,78 @@ describe MS::Mzml do
       string.gsub(/"mspire" version="([\.\d]+)"/, %Q{"mspire" version="X.X.X"})    
     end
 
+    it 'writes MS1 and MS2 spectra' do
+      # profile and ms_level 1
+      spec_params = ['MS:1000128', ['MS:1000511', 1]]
+
+      spec1 = MS::Mzml::Spectrum.new('scan=1', params: spec_params) do |spec|
+        spec.data_arrays = [[1,2,3], [4,5,6]]
+        spec.scan_list = MS::Mzml::ScanList.new do |sl|
+          scan = MS::Mzml::Scan.new do |scan|
+            # retention time of 42 seconds
+            scan.describe! ['MS:1000016', 40.0, 'UO:0000010']
+          end
+          sl << scan
+        end
+      end
+
+      # centroid,  ms_level 2, MSn spectrum, 
+      spec_params = ['MS:1000127', ['MS:1000511', 2], "MS:1000580"]
+
+      spec2 = MS::Mzml::Spectrum.new('scan=2', params: spec_params) do |spec| 
+        spec.data_arrays = [[1,2,3.5], [5,6,5]]
+        spec.scan_list = MS::Mzml::ScanList.new do |sl|
+          scan = MS::Mzml::Scan.new do |scan|
+            # retention time of 42 seconds
+            scan.describe! ['MS:1000016', 45.0, 'UO:0000010']
+          end
+          sl << scan
+        end
+        precursor = MS::Mzml::Precursor.new( spec1 )
+        si = MS::Mzml::SelectedIon.new
+        # the selected ion m/z:
+        si.describe! ["MS:1000744", 2.0]
+        # the selected ion charge state
+        si.describe! ["MS:1000041", 2]
+        # the selected ion intensity
+        si.describe! ["MS:1000042", 5]
+        precursor.selected_ions = [si]
+        spec.precursors = [precursor]
+      end
+
+      mzml = MS::Mzml.new do |mzml|
+        mzml.id = 'ms1_and_ms2'
+        mzml.cvs = MS::Mzml::CV::DEFAULT_CVS
+        mzml.file_description = MS::Mzml::FileDescription.new  do |fd|
+          fd.file_content = MS::Mzml::FileContent.new
+          fd.source_files << MS::Mzml::SourceFile.new
+        end
+        default_instrument_config = MS::Mzml::InstrumentConfiguration.new("IC",[], params: ['MS:1000031'])
+        mzml.instrument_configurations << default_instrument_config
+        software = MS::Mzml::Software.new
+        mzml.software_list << software
+        default_data_processing = MS::Mzml::DataProcessing.new("did_nothing")
+        mzml.data_processing_list << default_data_processing
+        mzml.run = MS::Mzml::Run.new("little_run", default_instrument_config) do |run|
+          spectrum_list = MS::Mzml::SpectrumList.new(default_data_processing)
+          spectrum_list.push(spec1, spec2)
+          run.spectrum_list = spectrum_list
+        end
+      end
+
+      #check = TESTFILES + '/ms/mzml/mspire_simulated.noidx.check.mzML'
+      tmpfile = TESTFILES + '/ms/mzml/mspire_simulated.MSn.TMP.mzML'
+      mzml.to_xml(tmpfile)
+      p tmpfile
+      #xml = sanitize_version(IO.read(tmpfile))
+      #xml.should be_a(String)
+      #sanitize_version(mzml.to_xml).should == xml
+      #xml.should == sanitize_version(IO.read(check))
+      #xml.should match(/<mzML/)
+      #File.unlink(tmpfile)
+    end
+
+
     it 'writes MS1 spectra and retention times' do
 
       spec_params = ['MS:1000127', ['MS:1000511', 1]]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.6.20
+  version: 0.6.21
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-02-24 00:00:00.000000000 Z
+date: 2012-02-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: &23959880 !ruby/object:Gem::Requirement
+  requirement: &8601020 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: *23959880
+  version_requirements: *8601020
 - !ruby/object:Gem::Dependency
   name: bsearch
-  requirement: &23959360 !ruby/object:Gem::Requirement
+  requirement: &8615260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: *23959360
+  version_requirements: *8615260
 - !ruby/object:Gem::Dependency
   name: andand
-  requirement: &23958860 !ruby/object:Gem::Requirement
+  requirement: &8612840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 1.3.1
   type: :runtime
   prerelease: false
-  version_requirements: *23958860
+  version_requirements: *8612840
 - !ruby/object:Gem::Dependency
   name: obo
-  requirement: &23958340 !ruby/object:Gem::Requirement
+  requirement: &8611480 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: 0.1.0
   type: :runtime
   prerelease: false
-  version_requirements: *23958340
+  version_requirements: *8611480
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &23974240 !ruby/object:Gem::Requirement
+  requirement: &8609880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: *23974240
+  version_requirements: *8609880
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &23973760 !ruby/object:Gem::Requirement
+  requirement: &8624220 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: *23973760
+  version_requirements: *8624220
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &23973280 !ruby/object:Gem::Requirement
+  requirement: &8617960 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *23973280
+  version_requirements: *8617960
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com
@@ -187,6 +187,7 @@ files:
 - lib/obo/unit.rb
 - lib/openany.rb
 - lib/write_file_or_string.rb
+- mspire.gemspec
 - obo/ims.obo
 - obo/ms.obo
 - obo/unit.obo