mspire 0.7.8 → 0.7.9

data/script/mzml_read_binary.rb

@@ -24,7 +24,7 @@ type = opts[:type].to_sym
 compressed = !opts[:not_compressed]
 
 ARGV.each do |base64|
-  puts MS::Mzml::DataArray.from_binary(base64, type, compressed).join(" ")
+  puts Mspire::Mzml::DataArray.from_binary(base64, type, compressed).join(" ")
 end
 
 

data/script/quant_compare_direct_injections.rb

@@ -0,0 +1,110 @@
+#!/usr/bin/env ruby
+
+require 'trollop'
+require 'mspire/mzml'
+require 'mspire/peak_list'
+require 'mspire/peak'
+
+DEFAULT_OUTFILE = "quant_compare.tsv"
+
+DEFAULTS = { 
+  :bin_width => Mspire::PeakList::DEFAULT_MERGE[:bin_width], 
+  :bin_unit => Mspire::PeakList::DEFAULT_MERGE[:bin_unit],
+}
+
+parser = Trollop::Parser.new do
+  banner "usage: #{File.basename(__FILE__)} <file>.mzML ..."
+  banner "output: #{DEFAULT_OUTFILE}"
+  banner ""
+  opt :outfile, "write results to this file", :default => DEFAULT_OUTFILE
+  opt :bin_width, "width of the bins for merging", :default => DEFAULTS[:bin_width]
+  opt :bin_unit, "units for binning (ppm or amu)", :default => DEFAULTS[:bin_unit].to_s
+  opt :sample_ids, "a yml file pointing basename to id", :type => :string
+end
+
+opts = parser.parse(ARGV)
+opts[:bin_unit] = opts[:bin_unit].to_sym
+
+if ARGV.size == 0
+  parser.educate 
+  exit
+end
+
+class TracedPeak < Array
+  # the m/z or x value
+  alias_method :x, :first
+  # the intensity or y value
+  alias_method :y, :last
+
+  def initialize(data, sample_id)
+    self[0] = data.first
+    self[1] = sample_id
+    self[2] = data.last
+  end
+
+  def sample_id
+    self[1]
+  end
+
+  def sample_id=(val)
+    self[1] = val
+  end
+end
+
+files = ARGV.dup
+
+peaklist = Mspire::PeakList.new
+
+if opts[:sample_ids]
+  basename_to_sample_id = YAML.load_file(opts[:sample_ids]) 
+end
+
+index_to_sample_id = {}
+sample_ids = files.each_with_index.map do |filename,index|
+  basename = filename.chomp(File.extname(filename))
+  sample_id = basename_to_sample_id ? basename_to_sample_id[basename] : basename
+  puts "processing: #{filename}"
+  Mspire::Mzml.open(filename) do |mzml|
+    mzml.each_with_index do |spec,i|
+      if spec.ms_level == 1
+        peaks = spec.peaks
+        #p peaks.size
+        peaks.each do |peak|
+          tp = TracedPeak.new(peak, index)
+          peaklist << tp
+        end
+      end
+    end
+  end
+  index_to_sample_id[index] = sample_id
+  sample_id
+end
+
+puts "gathered #{peaklist.size} peaks!"
+
+puts "sorting all peaks"
+peaklist.sort! 
+
+puts "merging peaks"
+#share_method = :greedy_y
+share_method = :share
+
+$VERBOSE = true
+data = Mspire::PeakList.merge([peaklist], opts.merge( {:only_data => true, :split => share_method} ))
+p data.size
+p data.first.size
+
+File.open(opts[:outfile],'w') do |out|
+
+  header = ["mzs", *sample_ids]
+  out.puts header.join("\t")
+
+  data.each do |bucket_of_peaks|
+    signal_by_sample_index = Hash.new {|h,k| h[k] = 0.0 }
+    mz = weighted_mz
+    row = [mz.round(6), *sample_ids.each_with_index.map {|id,index| signal_by_sample_index[index] }]
+    out.puts row.join("\t")
+  end
+end
+
+

data/spec/mspire/peak_list_spec.rb

@@ -25,28 +25,46 @@ describe Mspire::PeakList do
         mz += diff
       end
       @xs.map! {|mz| mz.round(2) }
-      @peaks = @xs.zip(@intensities).map {|pair| Mspire::Peak.new(pair) }
+      @peaks = @xs.zip(@intensities)
+    end
+
+    it 'outlines peak boundaries' do
+
+      peaklist = Mspire::PeakList[[5.08, 3]]
+      boundaries = peaklist.peak_boundaries
+      boundaries.should == [[0,0]]
+
+      peaklist = Mspire::PeakList[[5.08, 3], [5.09, 8]]
+      boundaries = peaklist.peak_boundaries
+      boundaries.should == [[0,1]]
+
+      peaklist = Mspire::PeakList[*@peaks]
+      boundaries = peaklist.peak_boundaries
+      #                      5        8     10       13 14       17     19       22 23       26  27
+      #act = [0, 3, 8, 9, 7, 2, 0, 0, 3, 8, 2, 9, 7, 1, 3, 0, 0, 10, 8, 2, 9, 7, 1, 3, 0, 0, 10, 8, 0] 
+      boundaries.should == [[1, 5], [8, 10, 13, 14], [17, 19, 22, 23], [26, 27]]
+
+      # another case that was failing early on:
+      peaklist = Mspire::PeakList[[5.08, 3], [5.09, 8], [5.1, 2], [5.11, 9], [5.12, 7], [5.13, 1], [5.14, 3]]
+      boundaries = peaklist.peak_boundaries
+      boundaries.should == [[0,2,5,6]]
     end
 
     it 'splits on zeros by default' do
-      peak = Mspire::PeakList.new(@peaks) # <- maybe more like a collection of peaks, but PeakList is flexible
-      peaks = peak.split
-      peaks.size.should == 4
-      peaks.should == [
+      peaklist = Mspire::PeakList[*@peaks] # <- maybe more like a collection of peaks, but PeakList is flexible
+      split_peaklist = peaklist.split
+      split_peaklist.size.should == 4
+      split_peaklist.should == [
         [[50.01, 3], [50.02, 8], [50.03, 9], [50.04, 7], [50.05, 2]],
         [[50.08, 3], [50.09, 8], [50.1, 2], [50.11, 9], [50.12, 7], [50.13, 1], [50.14, 3]],
         [[50.17, 10], [50.18, 8], [50.19, 2], [50.2, 9], [50.21, 7], [50.22, 1], [50.23, 3]],
         [[50.26, 10], [50.27, 8]]
       ]
-      # returns local minima if asked
-      (peaks2, local_minima) = peak.split(false, true)
-      peaks2.should == peaks
-      local_minima.should == [[], [2, 5], [2, 5], []]
     end
 
     # which it should since zeros are the ultimate local min!
     it 'always cleans up surrounding zeros and does not split non-multipeaks' do
-      peak = Mspire::PeakList.new(@peaks[0,7])  # simple
+      peak = Mspire::PeakList[*@peaks[0,7]]  # simple
       [:share, :greedy_y].each do |multipeak_split_method|
         peaks = peak.split(multipeak_split_method)
         peaks.first.should be_an_instance_of(Mspire::PeakList)
@@ -54,58 +72,185 @@ describe Mspire::PeakList do
       end
     end
 
-    it 'does #split(:share) and shares the peak proportional to adjacent peaks' do
-      data = [[50.07, 0], [50.08, 3], [50.09, 8], [50.1, 2], [50.11, 9], [50.12, 7], [50.13, 1], [50.14, 3], [50.15, 0]]
-      multipeak1 = Mspire::PeakList.new( data )
+    describe 'splitting a peak_list that is a multipeak' do
+      subject do
+        Mspire::PeakList[[50.07, 0], [50.08, 3], [50.09, 8], [50.1, 2], [50.11, 9], [50.12, 7], [50.13, 1], [50.14, 3], [50.15, 0]]
+      end
+
+      it 'can split a multipeak' do
+        multipeak = Mspire::PeakList[[5.08, 3], [5.09, 8]]
+        peaklists = multipeak.split_contiguous(:greedy_y)
+        peaklists.should == [[5.08, 3], [5.09, 8]]
 
-      answer = [
-        [[50.08, 3], [50.09, 8], [50.1, (2*8.0/17)]], 
-        [[50.1, 2*9.0/17], [50.11, 9], [50.12, 7], [50.13, 0.7]],
-        [[50.13, 0.3], [50.14, 3]]
-      ]
-      multipeak1.split(:share).should == answer
+        multipeak = Mspire::PeakList[[5.08, 3]]
+        peaklists = multipeak.split_contiguous(:greedy_y)
+        peaklists.should == [[5.08, 3]]
 
-      answer = [
-        [[50.08, 3], [50.09, 8]], 
-        [[50.1, 2], [50.11, 9], [50.12, 7], [50.13, 1]], 
-        [[50.14, 3]]
-      ]
-      multipeak1.split(:greedy_y).should == answer
+        multipeak = Mspire::PeakList[[5.08, 3], [5.09, 8], [5.1, 2], [5.11, 9], [5.12, 7], [5.13, 1], [5.14, 3]]
+        peaklists = multipeak.split_contiguous(:greedy_y)
+        peaklists.all? {|pl| pl.should be_a(Mspire::PeakList) }
+        peaklists.should == [[[5.08, 3], [5.09, 8]], [[5.1, 2], [5.11, 9], [5.12, 7], [5.13, 1]], [[5.14, 3]]]
+
+        multipeak = Mspire::PeakList[[5.08, 3], [5.09, 8], [5.1, 2], [5.11, 9], [5.12, 7], [5.13, 1], [5.14, 3]]
+        peaklists = multipeak.split_contiguous(:share)
+        peaklists.all? {|pl| pl.should be_a(Mspire::PeakList) }
+        peaklists.should == [[[5.08, 3], [5.09, 8], [5.1, 2*(8.0/17)]], [[5.1, 2*(9.0/17)], [5.11, 9], [5.12, 7], [5.13, 7.0/10]], [[5.13, 3.0/10], [5.14, 3]]]
 
-      answer = [
-        [[50.08, 3], [50.09, 9], [50.1, 2]], 
-        [[50.11, 9], [50.12, 7], [50.13, 1]], 
-        [[50.14, 3]]
-      ] 
+      end
+
+      it 'does #split(:share) and shares the peak proportional to adjacent peaks' do
+        answer = [
+          [[50.08, 3], [50.09, 8], [50.1, (2*8.0/17)]], 
+          [[50.1, 2*9.0/17], [50.11, 9], [50.12, 7], [50.13, 0.7]],
+          [[50.13, 0.3], [50.14, 3]]
+        ]
+        subject.split(:share).should == answer
+      end
 
-      # test a tie -> goes left!
-      peaks = @peaks[7,9]
-      peaks[2] = Mspire::Peak.new([peaks[2][0], 9])
-      multipeak2 = Mspire::PeakList.new( peaks )
-      multipeak2.split(:greedy_y).should == answer
+      it 'does #split(:greedy_y) and gives the local min to highest adjacent peak' do
+
+        answer = [
+          [[50.08, 3], [50.09, 8]], 
+          [[50.1, 2], [50.11, 9], [50.12, 7], [50.13, 1]], 
+          [[50.14, 3]]
+        ]
+        subject.split(:greedy_y).should == answer
+
+      end
+
+      it '#split splits on whitespace by default' do
+        subject[4,0] = [Mspire::Peak.new([50.105, 0])]
+        subject.split.should == [[[50.08, 3], [50.09, 8], [50.1, 2]], [[50.11, 9], [50.12, 7], [50.13, 1], [50.14, 3]]]
+      end
+
+      it 'gives local min to left peaklist in event of a tie with #split(:greedy_y)' do
+        answer = [
+          [[50.08, 3], [50.09, 9], [50.1, 2]], 
+          [[50.11, 9], [50.12, 7], [50.13, 1]], 
+          [[50.14, 3]]
+        ]
+
+        # test a tie -> goes left!
+        peaks = @peaks[7,9]
+        peaks[2] = Mspire::Peak.new([peaks[2][0], 9])
+        multipeak2 = Mspire::PeakList[ *peaks ]
+        multipeak2.split(:greedy_y).should == answer
+      end
 
     end
   end
 
   describe '#merge' do
 
-    subject do  
+    def compare_peaklist_sets(set1, set2)
+      set1.zip(set2) do |pl1, pl2|
+        pl1.sort.should == pl2.sort
+      end
+    end
+
+    subject do
 
-      list1 = [[10.1, 1], [10.5, 2], [10.7, 3], [11.5, 4]]
-      list2 = [[10.11, 5], [10.49, 6], [10.71, 7], [11.48, 8]]
-      list3 = [[10.09, 9], [10.51, 10], [10.72, 11], [11.51, 12]]
+      list1 = [[9.1, 2], [10.5, 1], [10.7, 3], [13.5, 4]].map {|pair| Mspire::Peak.new pair }
+      list2 = [[9.11, 6], [10.49, 5], [10.71, 7], [13.48, 8]].map {|pair| Mspire::Peak.new pair }
+      list3 = [[9.09, 11], [10.51, 9], [10.72, 10], [13.51, 12]].map {|pair| Mspire::Peak.new pair }
 
       [list1, list2, list3].map {|peaks| Mspire::PeakList.new( peaks ) }
     end
 
-    it 'merges, giving exact weighted average m/z values for each cluster' do
-      (peaklist1, data) = Mspire::PeakList.merge(subject, :bin_width => 0.08, :bin_unit => :amu, :return_data => true)
-      peaklist2 = Mspire::PeakList.merge(subject, :bin_width => 0.08, :bin_unit => :amu)
+    it 'whether we ask for data back or not, the peaklist is equal' do
+      (peaklist1, data) = Mspire::PeakList.merge(subject, :bin_width => 0.08, :bin_unit => :amu, :return_data => true, :split => false) 
+      peaklist2 = Mspire::PeakList.merge(subject, :bin_width => 0.08, :bin_unit => :amu, :split => :zero)
       peaklist1.should == peaklist2
+
       peaks = [[10.097333333333331, 10.502222222222223, 10.713809523809525, 11.498333333333333], [5.0, 6.0, 7.0, 8.0]].transpose
-      peaklist1.should == Mspire::PeakList.new(peaks)
-      data.should == [[[10.1, 1], [10.11, 5], [10.09, 9]], [[10.5, 2], [10.49, 6], [10.51, 10]], [[10.7, 3], [10.71, 7], [10.72, 11]], [[11.5, 4], [11.48, 8], [11.51, 12]]] 
+      #compare_peaklist_sets(peaklist1, Mspire::PeakList.new(peaks))
+      #compare_peaklist_sets(data, [[[10.1, 1], [10.11, 5], [10.09, 9]], [[10.5, 2], [10.49, 6], [10.51, 10]], [[10.7, 3], [10.71, 7], [10.72, 11]], [[11.5, 4], [11.48, 8], [11.51, 12]]] )
+
     end
+
+    it 'gives one peak with large bin width' do
+      [true, false].zip([26.0, 78.0]) do |normalize, inten|
+        peak_list = Mspire::PeakList.merge(subject, :bin_width => 2.5, :bin_unit => :amu, :normalize => normalize, :split => :greedy_y)
+        peak_list.size.should == 1
+        peak_list.first.x.should be_within(0.00000000001).of(11.136153846153846)
+        peak_list.first.y.should == inten
+      end
+    end
+
+    it 'regardless of split method, the total intensity remains the same' do
+      (0.1..2.3).step(0.1).to_a.each do |bw|
+        tot_ints = [:zero, :split, :greedy_y].map do |splt|
+          peak_list = Mspire::PeakList.merge(subject, :bin_width => bw, :bin_unit => :amu, :split => :zero)
+          peak_list.map(&:y).reduce(:+)
+        end
+        tot_ints.all? {|v| tot_ints.first == v }.should be_true
+      end
+    end
+
+    it 'does not alter the original data in any way (for :greedy_y or :zero)' do
+      before = Marshal.load(Marshal.dump(subject))
+      subj = Marshal.load(Marshal.dump(subject))
+      [:zero, :greedy_y].each do |split_mthd|
+        Mspire::PeakList.merge(subj, :bin_width => 2.2, :bin_unit => :amu, :split => split_mthd, :return_data => true)
+        subj.should == before
+      end
+    end
+
+    [:zero, :share, :greedy_y].each do |methd|
+
+      it "gives reasonable m/z values with very small binwidths (#{methd})" do
+        expected = [[9.09, 3.6666666666666665], [9.1, 0.6666666666666666], [9.11, 2.0], [10.49, 1.6666666666666667], [10.5, 0.3333333333333333], [10.51, 3.0], [10.7, 1.0], [10.71, 2.3333333333333335], [10.72, 3.3333333333333335], [13.48, 2.6666666666666665], [13.5, 1.3333333333333333], [13.51, 4.0]]
+        bw = 0.001
+        peak_list = Mspire::PeakList.merge(subject, :bin_width => bw, :bin_unit => :amu, :split => methd)
+        peak_list.size.should == expected.size
+        expected.zip(peak_list) do |exp, act|
+          act.first.should == exp.first
+          act.last.should be_within(0.00000000001).of(exp.last)
+        end
+      end
+
+      it 'gives reasonable m/z values for large binwidths' do
+        bw = 2.2
+        peak_list = Mspire::PeakList.merge(subject, :bin_width => bw, :bin_unit => :amu, :split => methd)
+        (peak_list.last.x > 13.51).should_not be_true
+        (peak_list.size > 2).should_not be_true
+      end
+
+      it 'gives same total intensity' do
+        bw = 0.8
+        total_intensity = subject.inject(0.0) {|sum,peaklist| sum + peaklist.map(&:y).reduce(:+) }
+        peak_list, data = Mspire::PeakList.merge(subject, :bin_width => bw, :bin_unit => :amu, :split => methd, :normalize => false, :return_data => true)
+        after = peak_list.inject(0.0) {|sum,peak| sum + peak.y }
+        after.should be_within(0.00000001).of(total_intensity)
+      end
+
+      it 'gives reasonable m/z values for medium-large binwidths' do
+        expected = [[10.086296296296297, 18.0], [13.498333333333333, 8.0]]
+        bw = 1.3
+        peak_list = Mspire::PeakList.merge(subject, :bin_width => bw, :bin_unit => :amu, :split => methd)
+        expected.zip(peak_list) do |exp, act|
+
+          act.first.should == exp.first
+          act.last.should be_within(0.00000000001).of(exp.last)
+        end
+      end
+    end
+
+
+
+=begin
+      data = Mspire::PeakList.merge(subject, :bin_width => 1000, :bin_unit => :ppm, :only_data => true)
+      # just frozen, and checking for sanity, not checked for perfect, accuracy at this level:
+      data.should == [[[10.09, 9]], [[10.1, 1]], [[10.11, 5]], [[10.49, 6]], [[10.5, 2]], [[10.51, 10]], [[10.7, 3]], [[10.71, 7]], [[10.72, 11]], [[11.48, 8]], [[11.5, 4]], [[11.51, 12]]]
+
+      [[[10.1, 1], [10.09, 9], [10.11, 5]], [[10.49, 6], [10.5, 2]], [[10.5, 2], [10.51, 10]], [[10.7, 3], [10.71, 7], [10.72, 11]], [[11.48, 8], [11.5, 4]], [[11.5, 4], [11.51, 12]]]
+      #peaklist3 = Mspire::PeakList.merge(subject, :bin_width => 100, :bin_unit => :ppm)
+      #p peaklist3
+      peaklist4 = Mspire::PeakList.merge(subject, :bin_width => 1000, :bin_unit => :ppm, :normalize => false)
+      peaklist4.should == [[10.097333333333331, 15.0], [10.49111111111111, 6.75], [10.508888888888887, 11.25], [10.713809523809525, 21.0], [11.483333333333334, 9.6], [11.508333333333331, 14.4]] 
+=end
+
+
   end
 
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: mspire
 version: !ruby/object:Gem::Version
-  version: 0.7.8
+  version: 0.7.9
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-03-29 00:00:00.000000000 Z
+date: 2012-04-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: nokogiri
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23083440 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,15 +22,10 @@ dependencies:
         version: '1.5'
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '1.5'
+  version_requirements: *23083440
 - !ruby/object:Gem::Dependency
   name: bsearch
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23080720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -38,15 +33,10 @@ dependencies:
         version: 1.5.0
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.5.0
+  version_requirements: *23080720
 - !ruby/object:Gem::Dependency
   name: andand
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23078680 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,15 +44,10 @@ dependencies:
         version: 1.3.1
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.3.1
+  version_requirements: *23078680
 - !ruby/object:Gem::Dependency
   name: obo
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23076600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -70,15 +55,10 @@ dependencies:
         version: 0.1.0
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 0.1.0
+  version_requirements: *23076600
 - !ruby/object:Gem::Dependency
   name: builder
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23074560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -86,15 +66,10 @@ dependencies:
         version: 3.0.0
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 3.0.0
+  version_requirements: *23074560
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23073060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -102,15 +77,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.4.2
+  version_requirements: *23073060
 - !ruby/object:Gem::Dependency
   name: trollop
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23071860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -118,15 +88,21 @@ dependencies:
         version: 1.16.2
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  version_requirements: *23071860
+- !ruby/object:Gem::Dependency
+  name: uuid
+  requirement: &23070700 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: 1.16.2
+        version: 2.3.5
+  type: :runtime
+  prerelease: false
+  version_requirements: *23070700
 - !ruby/object:Gem::Dependency
   name: fftw3
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23068400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -134,15 +110,10 @@ dependencies:
         version: '0.3'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '0.3'
+  version_requirements: *23068400
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23066100 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -150,15 +121,10 @@ dependencies:
         version: '2.6'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '2.6'
+  version_requirements: *23066100
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &23063900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -166,12 +132,7 @@ dependencies:
         version: 1.5.2
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: 1.5.2
+  version_requirements: *23063900
 description: mass spectrometry proteomics, lipidomics, and tools, a rewrite of mspire,
   merging of ms-* gems
 email: jtprince@gmail.com
@@ -280,11 +241,11 @@ 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
 - script/mzml_read_binary.rb
+- script/quant_compare_direct_injections.rb
 - spec/cv/param_spec.rb
 - spec/mspire/bin_spec.rb
 - spec/mspire/cv/obo_spec.rb
@@ -372,7 +333,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.18
+rubygems_version: 1.8.15
 signing_key: 
 specification_version: 3
 summary: mass spectrometry proteomics, lipidomics, and tools