mspire 0.7.17 → 0.7.18

data/VERSION

@@ -1 +1 @@
-0.7.17
+0.7.18

data/script/quant_compare_direct_injections.rb

@@ -15,9 +15,9 @@ end
 DEFAULT_OUTFILE = "quant_compare.tsv"
 
 DEFAULTS = { 
-  :bin_width => Mspire::PeakList::DEFAULT_MERGE[:bin_width], 
-  :bin_unit => Mspire::PeakList::DEFAULT_MERGE[:bin_unit],
-  :split => Mspire::PeakList::DEFAULT_MERGE[:split],
+  :bin_width => Mspire::Peaklist::DEFAULT_MERGE[:bin_width], 
+  :bin_unit => Mspire::Peaklist::DEFAULT_MERGE[:bin_unit],
+  :split => Mspire::Peaklist::DEFAULT_MERGE[:split],
   :round_mz => 6,
   :round_intensity => 6,
   :mz_prefix => "mz"
@@ -52,8 +52,6 @@ end
 
 files = ARGV.dup
 
-peaklist = Mspire::PeakList.new
-
 if opts[:sample_ids]
   basename_to_sample_id = YAML.load_file(opts[:sample_ids]) 
 end
@@ -63,25 +61,27 @@ sample_ids = files.map do |filename|
   basename_to_sample_id ? basename_to_sample_id[basename] : basename
 end
 
-peaklists = files.map do |filename|
+peaklists = files.zip(sample_ids).map do |filename, sample_id|
   putsv "processing: #{filename}"
-  bunch_of_peaks = []
+  bunch_of_peaks = Mspire::Peaklist.new
   Mspire::Mzml.open(filename) do |mzml|
     mzml.each_with_index do |spec,i|
       if spec.ms_level == 1
-        bunch_of_peaks.push(*spec.peaks)
+        spec.mzs.zip(spec.intensities) do |mz, int|
+          bunch_of_peaks.push Mspire::TaggedPeak.new([mz, int], sample_id)
+        end
       end
     end
   end
-  peaklist.sort_by!(&:x)
-  peaklist
+  bunch_of_peaks.sort_by!(&:x)
+  bunch_of_peaks 
 end
 
 putsv "merging peaks"
 share_method = :greedy_y
 #share_method = :share
 
-ar_of_doublets = Mspire::PeakList.merge_and_deconvolve(peaklists, opts.merge( {:split => share_method, :return_data => true} ))
+ar_of_doublets = Mspire::Peaklist.merge_and_deconvolve(peaklists, opts.merge( {:split => share_method, :return_data => true, :have_tagged_peaks => true} ))
 
 File.open(opts[:outfile],'w') do |out|
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.7.17
+  version: 0.7.18
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-07-10 00:00:00.000000000 Z
+date: 2012-07-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
@@ -332,7 +332,7 @@ files:
 - spec/mspire/mzml/source_file_spec.rb
 - spec/mspire/mzml/spectrum_spec.rb
 - spec/mspire/mzml_spec.rb
-- spec/mspire/peak_list_spec.rb
+- spec/mspire/peaklist_spec.rb
 - spec/mspire/plms1_spec.rb
 - spec/mspire/quant/qspec_spec.rb
 - spec/mspire/spectrum_spec.rb
@@ -390,7 +390,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.24
+rubygems_version: 1.8.18
 signing_key: 
 specification_version: 3
 summary: mass spectrometry proteomics, lipidomics, and tools