mspire 0.3.9 → 0.4.2

data/specs/ms/msrun_spec.rb

@@ -2,13 +2,15 @@
 require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
 require 'ms/msrun'
 require 'ostruct'
+require 'fileutils'
+require 'ms/parser/mzxml'
 
 parsers = %w(AXML LibXML XMLParser Regexp REXML)
 
 XMLStyleParser::Parser_precedence.replace( %w(AXML)  )
 
 
-describe "an msrun with basic, non-spectral information", :shared => true do
+shared_examples_for "an msrun with basic, non-spectral information" do
   it 'knows the type and version of file' do
     @run.filetype.should == @info.filetype
     @run.version.should == @info.version
@@ -37,12 +39,11 @@ describe "an msrun with basic, non-spectral information", :shared => true do
   it 'has correct first two scans and last scan' do
     [0,1,-1].each do |i|
       @info.scans[i].each do |k,v|
-        if k == :precursors
-          v.zip( @run.scans[i].send(k) ) do |exp, act|
-            act.mz.should be_close(exp.mz, 0.000001)
-            #if act.intensity # intensity not guaranteed to exist!
-            #  act.intensity.should == exp.intensity
-            #end
+        testing = @run.scans[i].send(k)
+        if k == :precursor
+          testing.mz.should be_close(v.mz, 0.000001)
+          if testing.intensity # intensity not guaranteed to exist!
+            testing.intensity.should == v.intensity
           end
         else
           @run.scans[i].send(k).should == v
@@ -52,7 +53,7 @@ describe "an msrun with basic, non-spectral information", :shared => true do
   end
 end
 
-describe "an msrun with spectrum", :shared => true do
+shared_examples_for "an msrun with spectrum" do
 
   it 'has all scans with spectrum data' do
     @run.scans.size.should == @info.scan_count
@@ -68,26 +69,27 @@ describe "an msrun with spectrum", :shared => true do
     @run.start_and_end_mz(2).should == @info.start_and_end_mz2
   end
 
+  it_should_behave_like "an msrun with basic, non-spectral information"
+end
+
+# some xml formats have precursor intensities built in, some do not
+shared_examples_for "an msrun with precursor intensities" do 
+
   it "has correct prec inten for first two scans and last scan" do
     [0,1,-1].each do |i|
       if i == 0
-        # currently we do diff't things for ms_level 1 scans! is it nil or []
-        #@run.scans[i].precursors.should == []
-        #@run.scans[i].precursors.should be_nil
+        @run.scans[i].precursor.should be_nil
         next
       end
-      expected = @info.scans[i][:precursors]
-      @run.scans[i].precursors.zip(expected) do |act,exp|
-        act.mz.should be_close(exp.mz, 0.000001)
-        act.intensity.should == exp.intensity
-      end
+      expected = @info.scans[i][:precursor]
+      @run.scans[i].precursor.mz.should be_close(expected.mz, 0.000001)
+      @run.scans[i].precursor.intensity.should == expected.intensity
     end
   end
 
-  it_should_behave_like "an msrun with basic, non-spectral information"
 end
 
-describe 'a basic scan info generator', :shared => true do
+shared_examples_for 'a basic scan info generator' do
 
   def check_table(table, answer)
     answer.each do |k,v|
@@ -143,13 +145,13 @@ MzXML_version_1_info = MyOpenStruct.new do |info|
     :num => 2,
     :ms_level => 2,
     :time => 1.90,
-    :precursors => [MS::Precursor.new(:mz => 391.045410, :intensity => 6986078.0)]
+    :precursor => MS::Precursor.new(:mz => 391.045410, :intensity => 6986078.0)
   }
   info.scans[-1] = {
     :num => 3748,
     :ms_level => 2,
     :time => 5102.55,
-    :precursors => [MS::Precursor.new(:mz => 433.564941, :intensity => 481800.0)]
+    :precursor => MS::Precursor.new(:mz => 433.564941, :intensity => 481800.0)
   }
   info.scan_count0 = info.scan_count
   info.scan_count1 = 937
@@ -163,7 +165,7 @@ describe MS::MSRun, "on mzXML version 1 files (w/o spectra)" do
     before(:all) do
       @info = MzXML_version_1_info
       start = Time.now
-      @run = @info.klass.new(@info.file, :spectra => false)
+      @run = @info.klass.new(@info.file, :lazy => :no_spectra)
       puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
     end
     it_should_behave_like "an msrun with basic, non-spectral information"
@@ -176,34 +178,35 @@ describe MS::MSRun, "on mzXML version 1 files (w/spectra)" do
     before(:all) do
       @info = MzXML_version_1_info
       start = Time.now
-      @run = @info.klass.new(@info.file)
+      @run = @info.klass.new(@info.file, :lazy => :not)
       puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
     end
 
     it_should_behave_like "an msrun with spectrum"
+    it_should_behave_like "an msrun with precursor intensities"
     it_should_behave_like 'a basic scan info generator'
   end
 end
 
 MzXML_version_20_info = MyOpenStruct.new do |info|
-  info.file = Tfiles_l + '/opd1_2runs_2mods/data/020.readw.mzXML'
+  info.file = Tfiles + '/opd1_2runs_2mods/data/020.readw.mzXML'
   info.klass = MS::MSRun
   info.filetype = :mzxml
   info.version = '2.0'
-  info.scan_count = 3620
+  info.scan_count = 20
   #info.scan_counts = ??
   info.start_time = 0.13
-  info.end_time = 5099.69
+  info.end_time = 27.31
   info.num_to_prec_mz_hash = {
     0 => nil,
     1 => nil,
     2 => 390.9291992,
     3 => 1121.944824,
     4 => 1321.913574,
-    3617 => nil,
-    3618 => 828.2867432,
-    3619 => 424.8538208,
-    3620 => 357.0411987,
+    17 => nil,
+    18 => 308.795959,
+    19 => 444.983337,
+    20 => 361.671875,
   }
   info.scans = {}
   info.scans[0]= {
@@ -215,61 +218,80 @@ MzXML_version_20_info = MyOpenStruct.new do |info|
     :num => 2,
     :ms_level => 2,
     :time => 1.49,
-    :precursors => [MS::Precursor.new(:mz => 390.9291992, :intensity => 8.14409e+006)]
+    :precursor => MS::Precursor.new(:mz => 390.9291992, :intensity => 8.14409e+006)
   }
   info.scans[-1] = {
-    :num => 3620,
+    :num => 20,
     :ms_level => 2,
-    :time => 5099.69,
-    :precursors => [MS::Precursor.new(:mz => 357.0411987, :intensity => 643017.0)]
+    :time => 27.31,
+    :precursor => MS::Precursor.new(:mz => 361.671875, :intensity => 572148.0)
   }
   info.scan_count0 = info.scan_count
-  info.scan_count1 = 905
-  info.scan_count2 = 2715
-  info.start_and_end_mz1 = [300.0, 1500.0]
+  info.scan_count1 = 5
+  info.scan_count2 = 15
+  info.start_and_end_mz1 = [300.0, 1499]  # apparently nothing brushes right up to 1500
   # that first number on start_and_end_mz2 is a arbitrary as to accuracy...
   # I'm not sure the correct answer
-  info.start_and_end_mz2 = [110.0, 2000.0] 
+  info.start_and_end_mz2 = [110.0, 1955]  ## again, this is based on data
 end
 
 describe MS::MSRun, "on mzXML version 2.0 files (w/o spectra)" do
-  spec_large do
-    before(:all) do
-      @info = MzXML_version_20_info
-      start = Time.now
-      @run = @info.klass.new(@info.file, :spectra => false)
-      puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
-    end
+  before(:all) do
+    @info = MzXML_version_20_info
+    start = Time.now
+    @run = @info.klass.new(@info.file, :lazy => :no_spectra)
+    puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
+  end
 
-    it_should_behave_like "an msrun with basic, non-spectral information"
-    it_should_behave_like 'a basic scan info generator'
+  #it_should_behave_like "an msrun with basic, non-spectral information"
+  it_should_behave_like 'a basic scan info generator'
+
+  it 'fixes bad scan tags on the fly!' do
+    # if this test works, this is true
   end
 end
 
-describe MS::MSRun, "on mzXML version 2.0 files (w/spectra)" do
-  spec_large do
-    before(:all) do
-      @info = MzXML_version_20_info
-      start = Time.now
-      @run = @info.klass.new(@info.file)
-      puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
-    end
+shared_examples_for "an mzXML version 2.0 file (w/spectra)" do
+  before(:all) do
+    @info = MzXML_version_20_info
+    # first fix the file of bad scan tags
+    @info.file
+    #start = Time.now
+    @fh = File.open(@info.file)
+    @run = @info.klass.new(@fh, :lazy => @lazy_type)
+    #puts "- read #{File.basename(@new_file)} in #{Time.now - start} seconds" if $specdoc
+  end
 
-    it_should_behave_like "an msrun with spectrum"
-    it_should_behave_like 'a basic scan info generator'
+  after(:all) do
+    # @fh.close  # not sure why, but the filehandle is already closed!
+    # Maybe because the filehandle went out of scope??
   end
+
+  it_should_behave_like "an msrun with spectrum"  # <- trouble
+  it_should_behave_like 'a basic scan info generator'
 end
 
+#[:io, :string, :not].each do |lazy_type|
+[:io, :string, :not].each do |lazy_type|
+  describe MS::MSRun, "mzXML v2.0 with :lazy => :#{lazy_type}" do 
+    before(:all) { @lazy_type = lazy_type}
+    it_should_behave_like "an mzXML version 2.0 file (w/spectra)"
+  end
+
+ end
+  
 Mzdata_105_info = MyOpenStruct.new do |info|
-  info.file = Tfiles_l + '/opd1_2runs_2mods/data/020.mzData.xml'
+  info.file = Tfiles + '/opd1_2runs_2mods/data/020.mzData.xml'
   info.klass = MS::MSRun
   info.filetype = :mzdata
   info.version = '1.05'
-  info.scan_count = 3619  # this should be 3620, they drop the last scan
+  # NOTE that the real file drops the last scan!!  giving a mismatch
+  info.scan_count = 20  
   info.start_time = 0.13002   # minutes == 0.00216667
   # This is the correct one!, but Thermo drops last scan
   # info.end_time = 5099.688    #84.9948
-  info.end_time = 84.968500*60  #   5098.11
+  #info.end_time = 84.968500*60  #   5098.11
+  info.end_time = 0.455167 * 60 
 
   info.num_to_prec_mz_hash = {
     0 => nil,
@@ -277,9 +299,10 @@ Mzdata_105_info = MyOpenStruct.new do |info|
     2 => 390.9291992,
     3 => 1121.944824,
     4 => 1321.913574,
-    3617 => nil,
-    3618 => 828.2867432,
-    3619 => 424.8538208,
+    17 => nil,
+    18 => 308.795959,
+    19 => 444.983337,
+    20 =>  361.671875,
     # 3620 => 357.0411987, Bioworks 3.3 is broken
   }
 
@@ -293,105 +316,124 @@ Mzdata_105_info = MyOpenStruct.new do |info|
     :num => 2,
     :ms_level => 2,
     :time => 0.024833 * 60,   # 1.48998
-    :precursors => [MS::Precursor.new( :mz => 390.9291992, :intensity => 8.144094e+006) ],
+    :precursor => MS::Precursor.new( :mz => 390.9291992, :intensity => 8.144094e+006),
   }
   info.scans[-1] = {
-    :num => 3619,
+    :num => 20,
     :ms_level => 2,
     #:time => 5099.69, 
-    :time => 84.968500 * 60,  #   5098.11
+    #:time => 84.968500 * 60,  #   5098.11
+    :time => 0.455167 * 60,
 
-    :precursors => [MS::Precursor.new( :mz => 424.853821, :intensity => 738590.0 )] # wrong
+    :precursor => MS::Precursor.new( :mz => 361.671875, :intensity => 572148.0 ) # wrong
   }
   info.scan_count0 = info.scan_count
-  info.scan_count1 = 905
-  info.scan_count2 = 2714  # should be 2715, they dropped the last scan!
+  info.scan_count1 = 5
+  info.scan_count2 = 15 # should be 2715, they dropped the last scan!
   info.start_and_end_mz1 = [300.0, 1500.0]
   # This is the Correct one!!!, but Thermo drops last scan
   #info.start_and_end_mz2 = [112.0, 2000.0] 
-  info.start_and_end_mz2 = [95.0, 2000.0]
+  info.start_and_end_mz2 = [95.0, 1955]
 end
 
 describe MS::MSRun, "on mzData version 1.05 files (Bioworks3.3) (w/o spectra)" do
-  spec_large do
-    before(:all) do
-      @info = Mzdata_105_info
-      start = Time.now
-      @run = @info.klass.new(@info.file, :spectra => false)
-      puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
-      puts "- [NOTE] mzData files from Thermo are missing their last scan!" if $specdoc
-    end
+  before(:all) do
+    @info = Mzdata_105_info
+    start = Time.now
+    @run = @info.klass.new(@info.file, :lazy => :no_spectra)
+    puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
+    puts "- [NOTE] mzData files from Thermo are missing their last scan!" if $specdoc
+  end
 
-    it_should_behave_like "an msrun with basic, non-spectral information"
-    it_should_behave_like 'a basic scan info generator'
+  it_should_behave_like "an msrun with basic, non-spectral information"
+  it_should_behave_like 'a basic scan info generator'
 
-  end
 end
 
-describe MS::MSRun, "on mzData version 1.05 files (Bioworks3.3) (w/spectra)" do
-  spec_large do
-    before(:all) do
-      @info = Mzdata_105_info  
-      start = Time.now
-      @run = @info.klass.new(@info.file)
-      puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
-      puts "- [NOTE] mzData files from Thermo are missing their last scan!" if $specdoc
-    end
+shared_examples_for "mzData v1.05 (Bioworks3.3) (w/spectra)" do
+  before(:all) do
+    @info = Mzdata_105_info  
+    #start = Time.now
+    @fh = File.open(@info.file)
+    @run = @info.klass.new(@fh, :lazy => @lazy_type)
+    #puts "- read #{File.basename(@info.file)} in #{Time.now - start} seconds" if $specdoc
+    puts "- [NOTE] mzData files from Thermo are missing their last scan!" if $specdoc
+  end
 
-    it_should_behave_like "an msrun with spectrum"
-    it_should_behave_like 'a basic scan info generator'
+  it_should_behave_like "an msrun with spectrum"
+  it_should_behave_like 'a basic scan info generator'
 
-    it 'gets correct precursor intensities for all scans' do
-      check_file = Tfiles_l + '/opd1_2runs_2mods/data/020.readw.mzXML'
-      prec_inten_mzs = IO.readlines(check_file).grep(/precursorMz/).map do |line|
-        if line =~ /Intensity="([\d\.e\+\-]+)">([\d\.e\+\-]+)</
-          [$1.to_f, $2.to_f]
-        else
-          abort "didn't match for some crazy reason! (probably newline issues)"
-        end
+  it 'has (or can get) correct precursor intensities for all scans' do
+    check_file = Tfiles + '/opd1_2runs_2mods/data/020.readw.mzXML'
+    prec_inten_mzs = IO.readlines(check_file).grep(/precursorMz/).map do |line|
+      if line =~ /Intensity="([\d\.e\+\-]+)">([\d\.e\+\-]+)</
+        [$1.to_f, $2.to_f]
+      else
+        abort "didn't match for some crazy reason! (probably newline issues)"
       end
+    end
 
-      prec_mz_cnt = 0
-      @run.scans.each_with_index do |scan,i|
-        next if i % 4 == 0
-        (exp_int, exp_mz) = prec_inten_mzs[prec_mz_cnt] 
+    prec_mz_cnt = 0
+    @run.scans.each_with_index do |scan,i|
+      next if i % 4 == 0
+      (exp_int, exp_mz) = prec_inten_mzs[prec_mz_cnt] 
 
-        precursor = scan.precursors.first
-        precursor.mz.should be_close(exp_mz, 0.00001)
-        precursor.intensity.should be_close(exp_int, 51)
+      precursor = scan.precursor
+      precursor.mz.should be_close(exp_mz, 0.00001)
+      prec_inten = 
+        if precursor.intensity.nil?
+          precursor.parent.spectrum.intensity_at_mz(precursor.mz)
+        else
+          precursor.intensity
+        end
+      prec_inten.should be_close(exp_int, 51)
 
-        prec_mz_cnt += 1
-      end
+      prec_mz_cnt += 1
+    end
   end
 end
+
+#[:string, :not, :io].each do |lazy_type|
+[:io].each do |lazy_type|
+ describe MS::MSRun, "mzData v1.05 with :lazy => :#{lazy_type}" do 
+    before(:all) { @lazy_type = lazy_type}
+    it_should_behave_like "mzData v1.05 (Bioworks3.3) (w/spectra)"
+  end
 end
 
-describe MS::MSRun, 'with small file of twenty scans' do
-  before(:each) do
+describe 'reading a small file of twenty scans' do
+  before(:all) do
     @file = Tfiles + "/opd1/twenty_scans.mzXML"
-    @msrun = MS::MSRun.new(@file)
   end
 
-  it 'retrieves times and spectra' do
-    (times, spectra) = @msrun.times_and_spectra(1)
-    etimes = %w(0.440000 5.150000 10.690000 16.400000 22.370000).map {|t| t.to_f }
-    num_peaks = [992, 814, 796, 849, 813]
-    tol = 0.000000001
-    spectra[0].mz[1].should be_close(301.430114746094, tol)
-    spectra[0].intensity[1].should be_close(22192.0, tol)
-    spectra[0].mz[-1].should be_close(1499.09912109375, tol)
-    spectra[0].intensity[-1].should be_close(111286.0, tol)
-
-    spectra[-1].mz[1].should be_close(301.243774414062, tol)
-    spectra[-1].intensity[1].should be_close(77503.0, tol)
-    spectra[-1].mz[-1].should be_close(1499.42016601562, tol)
-    spectra[-1].intensity[-1].should be_close(13.0, tol)
-
-    num_peaks.each_with_index do |n,i|
-      spectra[i].mz.size.should == n
-    end
-    etimes.each_with_index do |t,i|
-      times[i].should be_close(t, 0.00001)
+  it 'retrieves times and spectra with all lazy types' do
+    [:not, :string, :io].each do |lazy_type|
+
+      File.open(@file) do |io|
+        msrun = MS::MSRun.new(io, :lazy => lazy_type)
+
+
+        (times, spectra) = msrun.times_and_spectra(1)
+        etimes = %w(0.440000 5.150000 10.690000 16.400000 22.370000).map {|t| t.to_f }
+        num_peaks = [992, 814, 796, 849, 813]
+        tol = 0.000000001
+        spectra[0].mzs[1].should be_close(301.430114746094, tol)
+        spectra[0].intensities[1].should be_close(22192.0, tol)
+        spectra[0].mzs[-1].should be_close(1499.09912109375, tol)
+        spectra[0].intensities[-1].should be_close(111286.0, tol)
+
+        spectra[-1].mzs[1].should be_close(301.243774414062, tol)
+        spectra[-1].intensities[1].should be_close(77503.0, tol)
+        spectra[-1].mzs[-1].should be_close(1499.42016601562, tol)
+        spectra[-1].intensities[-1].should be_close(13.0, tol)
+
+        num_peaks.each_with_index do |n,i|
+          spectra[i].mzs.size.should == n
+        end
+        etimes.each_with_index do |t,i|
+          times[i].should be_close(t, 0.00001)
+        end
+      end
     end
   end
 end
@@ -412,9 +454,10 @@ describe MS::MSRun, 'with a small set of scans' do
     precs = (0..(vals.size)).to_a.map do |x|
       MS::Precursor.new([x,100])
     end
+
     scans = vals.zip(precs).map do |ar,prec|
       scan = MS::Scan.new(ar)
-      scan.precursors = [prec]
+      scan.precursor = prec
       scan
     end
     scans.size.should == vals.size
@@ -422,7 +465,7 @@ describe MS::MSRun, 'with a small set of scans' do
     parents = [nil,s[0],s[0],s[2],s[2],nil,s[5],s[6],s[5]]
     MS::MSRun.add_parent_scan(scans)
     scans.each_with_index do |scan,i|
-      scan.precursors.first.parent.should == parents[i]
+      scan.precursor.parent.should == parents[i]
     end
   end
 end

data/specs/ms/parser_spec.rb

@@ -22,7 +22,7 @@ describe "a MS::Parser on a file", :shared => true do
 
   ########################################################################
   # NOTE: methods to verify parsing of information should be defined where
-  # that information is require.
+  # that information is required.
   # e.g. msrun_spec.rb will verify that msrun objects are created properly.
   # this is because we don't care how we get that file, just that we get it.
   # The whole process of parsing a file should be transparent to users.
@@ -71,7 +71,7 @@ describe MS::Parser, "on an mzXML version 2 file" do
       @version = '2.0'
       @filetype_version = [@filetype, @version]
       @subclass = 'MS::Parser::MzXML'
-      @file = Tfiles_large + '/opd1_2runs_2mods/data/020.readw.mzXML'
+      @file = Tfiles + '/opd1_2runs_2mods/data/020.readw.mzXML'
     end
     it_should_behave_like "a MS::Parser on a file"
   end
@@ -84,7 +84,7 @@ describe MS::Parser, "on an mzData version 1.05 file" do
       @version = '1.05'
       @filetype_version = [@filetype, @version]
       @subclass = 'MS::Parser::MzData'
-      @file = Tfiles_large + '/opd1_2runs_2mods/data/020.mzData.xml'
+      @file = Tfiles + '/opd1_2runs_2mods/data/020.mzData.xml'
     end
     it_should_behave_like "a MS::Parser on a file"
   end

data/specs/ms/spectrum_spec.rb

@@ -59,8 +59,6 @@ describe MS::Spectrum, 'of full values' do
     @spec.index(1029.212891).should == 597
   end
 
-
-
 end
 
 

data/specs/spec_id/precision/filter_spec.rb

@@ -146,7 +146,7 @@ describe 'filtering on a real srf file' do
   spec_large do
     it 'does tmm with a toppred file on srf' do
       opts = {:sequest => {:xcorr1 => 1.0, :xcorr2 => 1.0, :xcorr3 => 1.0, :deltacn => 0.1, :ppm => 1000.0, :include_deltacnstar => false}}
-      dir = Tfiles_l + '/opd1_2runs_2mods/sequest'
+      dir = Tfiles_l + '/opd1_2runs_2mods/sequest33'
       tmm_file = dir + '/ecoli_K12_ncbi_20060321.toppred.xml'
       fasta_file = dir + '/ecoli_K12_ncbi_20060321.fasta'
       sequest_file = dir + '/ecoli.params'
@@ -219,6 +219,9 @@ describe SpecID::Precision::Filter::Peps do
       [1.2, 1.2, 1.2, 0.1, 50, true] => 6, # "all passing"
       [1.2, 1.2, 1.2, 0.2, 50, true] => 1, # "high deltacn"
       [1.0, 1.0, 1.6, 0.1, 50, true] => 5, # "one xcorr too high"
+      ## 
+      [1.0, 1.0, 1.0, 0.05, 60, true] => 6,  ## testing ppm filtering:
+      [1.0, 1.0, 1.0, 0.05, 10, true] => 0,
     }
     args_and_expected.each do |args,exp|
       filt = SpecID::Precision::Filter::Peps.new(:standard_sequest_filter, *args)

data/specs/spec_id/precision/prob_spec.rb

@@ -28,14 +28,14 @@ describe 'finding precision Proph::Prot::Pep objects' do
 
   it 'runs without any validator' do
     answer = SpecID::Precision::Prob.new.precision_vs_num_hits(@spec_id) 
-    answer.keys.map {|v| v.to_s }.sort.should == ["aaseqs", "charges", "count", "params", "pephits_precision", "probabilities"]
+    answer.keys.map {|v| v.to_s }.sort.should == ["aaseqs", "charges", "count", "params", "pephits", "pephits_precision", "probabilities"]
     answer[:aaseqs].should == %w(3 0 4 1 2)
   end
 
   it 'returns modified peptides if any modified peptides' do
     @spec_id.peps[1].mod_info = Sequest::PepXML::SearchHit::ModificationInfo.new(['MODIFIED', []])
     answer = SpecID::Precision::Prob.new.precision_vs_num_hits(@spec_id) 
-    answer.keys.map {|v| v.to_s }.sort.should == ["aaseqs", "charges", "count", "modified_peptides", "params", "pephits_precision", "probabilities"]
+    answer.keys.map {|v| v.to_s }.sort.should == ["aaseqs", "charges", "count", "modified_peptides", "params", "pephits", "pephits_precision", "probabilities"]
   end
 
 end

data/specs/spec_id/sequest/pepxml_spec.rb

@@ -309,7 +309,7 @@ describe 'bioworks file with modifications transformed into pepxml' do
 
   spec_large do
     before(:all) do
-      modfiles_sequest_dir = Tfiles_l + '/opd1_2runs_2mods/sequest/'
+      modfiles_sequest_dir = Tfiles_l + '/opd1_2runs_2mods/sequest33/'
       modfiles_data_dir = Tfiles_l + '/opd1_2runs_2mods/data/'
       @srgfile = modfiles_sequest_dir + 'tmp.srg'
       @out_path = modfiles_sequest_dir + 'pepxml'

data/specs/spec_id/sqt_spec.rb

@@ -110,7 +110,7 @@ describe 'converting a large srf to sqt' do
       del(@output)
     end
     it 'can get db info with correct path' do
-      @srf.to_sqt(@output, :db_info => true, :new_db_path => Tfiles_l + '/opd1_2runs_2mods/sequest')
+      @srf.to_sqt(@output, :db_info => true, :new_db_path => Tfiles_l + '/opd1_2runs_2mods/sequest33')
       @output.exist_as_a_file?.should be_true
       lines = IO.readlines(@output)
       has_md5 = lines.any? do |line|
@@ -127,8 +127,8 @@ describe 'converting a large srf to sqt' do
       del(@output)
     end
     it 'can update the Database' do
-      @srf.to_sqt(@output, :new_db_path => Tfiles_l + '/opd1_2runs_2mods/sequest', :update_db_path => true)
-      regexp = Regexp.new("Database\t/.*/opd1_2runs_2mods/sequest/ecoli_K12_ncbi_20060321.fasta")
+      @srf.to_sqt(@output, :new_db_path => Tfiles_l + '/opd1_2runs_2mods/sequest33', :update_db_path => true)
+      regexp = Regexp.new("Database\t/.*/opd1_2runs_2mods/sequest33/ecoli_K12_ncbi_20060321.fasta")
       updated_db = IO.readlines(@output).any? do |line|
         line =~ regexp
       end
@@ -217,8 +217,8 @@ end
 describe SQTGroup, ': acting as a SpecID on large files' do
   spec_large do 
     before(:each) do
-      file1 = Tfiles_l + '/opd1_2runs_2mods/sequest/020.sqt'
-      file2 = Tfiles_l + '/opd1_2runs_2mods/sequest/040.sqt'
+      file1 = Tfiles_l + '/opd1_2runs_2mods/sequest33/020.sqt'
+      file2 = Tfiles_l + '/opd1_2runs_2mods/sequest33/040.sqt'
       file1.exist_as_a_file?.should be_true
       file2.exist_as_a_file?.should be_true
       @sqg = SQTGroup.new([file1, file2])