mspire 0.2.4 → 0.3.0

data/specs/gi_spec.rb

@@ -0,0 +1,22 @@
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper'
 )
+require 'gi'
+
+
+describe GI, "given a 'GI' number" do
+  before(:all) do
+    @gi_num = 836805
+  end
+  it 'can query NCBI for annotation (fails nicely w/o connection)' do
+    annot = GI.gi2annot([@gi_num])
+    if annot
+      annot.first.should == 'proteosome component PRE4 [Saccharomyces cerevisiae]'
+    else
+      puts "- retrieval of gi failed gracefully w/o internet connection"
+    end
+end
+
+end
+
+
+
+

data/specs/load_bin_path.rb

@@ -0,0 +1,7 @@
+tmp = $VERBOSE ; $VERBOSE = nil
+LOAD_BIN_PATH = File.expand_path(File.dirname(__FILE__) + "#{File::SEPARATOR}..#{File::SEPARATOR}bin")
+$VERBOSE = tmp
+
+if ENV.key?("PATH")
+  ENV["PATH"] =  LOAD_BIN_PATH + File::PATH_SEPARATOR + ENV["PATH"]
+end

data/specs/merge_deep_spec.rb

@@ -0,0 +1,13 @@
+require File.expand_path( File.dirname(__FILE__) + '/spec_helper' )
+require 'merge_deep'
+
+describe 'merging one level deep' do
+  it 'works' do
+    base = {1=>"X", 3=>{6=>7, 8=>9}}
+    another = {1=>'y', 3=>{6=>9}}
+    ans = base.merge_deep(another, 1)
+    ans.should == {1=>'y', 3=>{6=>9, 8=>9}}
+  end
+end
+
+

data/specs/ms/gradient_program_spec.rb

@@ -0,0 +1,77 @@
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require 'ms/gradient_program'
+
+describe GradientProgram do
+  it 'can be set from a Thermo Xcal 2.X .meth file' do
+    data = [
+      [0.00, 95.0, 5.0, 0.0, 0.0, 38.0],
+      [1.00, 90.0, 10.0, 0.0, 0.0, 38.0],
+      [30.00, 85.0, 15.0, 0.0, 0.0, 38.0],
+      [40.00, 80.0, 20.0, 0.0, 0.0, 38.0],
+      [45.00, 78.0, 22.0, 0.0, 0.0, 38.0],
+      [50.00, 72.0, 28.0, 0.0, 0.0, 38.0],
+      [65.00, 60.0, 40.0, 0.0, 0.0, 38.0],
+      [72.00, 10.0, 90.0, 0.0, 0.0, 38.0],
+      [75.0, 10.0, 90.0, 0.0, 0.0, 38.0],
+      [81.00, 10.0, 90.0, 0.0, 0.0, 38.0],
+      [81.10, 95.0, 5.0, 0.0, 0.0, 38.0],
+      [90.00, 95.0, 5.0, 0.0, 0.0, 38.0],
+    ]
+
+    ms_pump_expected_tps = data.map do |ar| 
+      GradientProgram::TimePoint.new(ar[0], ar[-1], ar[1,4])
+    end
+    ms_pump_expected = GradientProgram.new('MS Pump', ms_pump_expected_tps, %w(A B C D))
+
+    data = [
+      [0.00, 0.0, 0.0, 100.0, 0.0, 40.0],
+      [90.0, 0.0, 0.0, 100.0, 0.0, 40.0],
+    ]
+    sample_pump_expected_tps = data.map {|ar| GradientProgram::TimePoint.new(ar[0], ar[-1], ar[1,4]) }
+    sample_pump_expected = GradientProgram.new('Sample Pump', sample_pump_expected_tps, %w(A B C D))
+
+    file = Tfiles + '/s01_anC1_ld020mM.meth'
+    File.open(file) do |fh|
+      gps = GradientProgram.all_from_handle(fh)
+      gps[0].should == ms_pump_expected
+      gps[1].should == sample_pump_expected
+    end
+  end
+
+  it 'can be set from a Thermo Xcal 1.X .RAW file (but missing pump_type)' do
+    file = Tfiles + '/opd1_020_beginning.RAW'
+    data = [[0.0, 0.0, 0.0, 100.0, 0.0, 200.0],
+      [1.0, 0.0, 0.0, 96.0, 4.0, 200.0],
+      [10.0, 0.0, 0.0, 96.0, 4.0, 200.0],
+      [11.0, 0.0, 0.0, 100.0, 0.0, 200.0],
+      [85.0, 0.0, 0.0, 100.0, 0.0, 200.0],]
+
+    time_points = data.map do |ar| 
+      GradientProgram::TimePoint.new(ar[0], ar[-1], ar[1,4])
+    end
+    pump_type = ''  ## need to get pump type...
+    ms_pump_expected = GradientProgram.new(pump_type, time_points, %w(A B C D))
+
+    data = [[0.0, 95.0, 5.0, 0.0, 0.0, 200.0],
+      [1.0, 95.0, 5.0, 0.0, 0.0, 200.0],
+      [61.0, 55.0, 45.0, 0.0, 0.0, 200.0],
+      [62.0, 5.0, 95.0, 0.0, 0.0, 200.0],
+      [67.0, 5.0, 95.0, 0.0, 0.0, 200.0],
+      [68.0, 95.0, 5.0, 0.0, 0.0, 200.0],
+      [85.0, 95.0, 5.0, 0.0, 0.0, 200.0],]
+    time_points = data.map do |ar| 
+      GradientProgram::TimePoint.new(ar[0], ar[-1], ar[1,4])
+    end
+    pump_type = ''  ## need to get pump type...
+    sample_pump_expected = GradientProgram.new(pump_type, time_points, %w(A B C D))
+
+    # we'd like to get an older .meth file to do this on
+    File.open(file) do |fh|
+      gps = GradientProgram.all_from_handle(fh)
+      gps[0].should == ms_pump_expected
+      gps[1].should == sample_pump_expected
+
+    end
+  end
+
+end

data/specs/ms/msrun_spec.rb

@@ -0,0 +1,455 @@
+
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require 'ms/msrun'
+require 'ostruct'
+
+parsers = %w(AXML LibXML XMLParser Regexp REXML)
+
+XMLStyleParser::Parser_precedence.replace( %w(AXML)  )
+
+
+describe "an msrun with basic, non-spectral information", :shared => true do
+  it 'knows the type and version of file' do
+    @run.filetype.should == @info.filetype
+    @run.version.should == @info.version
+  end
+
+  it 'knows basic run information' do
+    @run.scan_count.should == @info.scan_count
+    @run.start_time.should == @info.start_time
+    @run.end_time.should == @info.end_time
+  end
+
+  it 'has all scans' do
+    @run.scans.size.should == @info.scan_count
+    @run.scans.each_with_index do |sc,i|
+      sc.class.should == MS::Scan
+    end
+  end
+
+  it 'can determine scan counts for any mslevel' do
+    @run.scan_counts.class.should == Array
+    @run.scan_count(0).should == @info.scan_count0
+    @run.scan_count(1).should == @info.scan_count1
+    @run.scan_count(2).should == @info.scan_count2
+  end
+
+  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
+          end
+        else
+          @run.scans[i].send(k).should == v
+        end
+      end
+    end
+  end
+end
+
+describe "an msrun with spectrum", :shared => true do
+
+  it 'has all scans with spectrum data' do
+    @run.scans.size.should == @info.scan_count
+    @run.scans.each_with_index do |sc,i|
+      sc.class.should == MS::Scan
+      sc.spectrum.should have_mz_data
+      sc.spectrum.should have_intensity_data
+    end
+  end
+
+  it 'can determine start_and_end_mz' do
+    @run.start_and_end_mz(1).should == @info.start_and_end_mz1
+    @run.start_and_end_mz(2).should == @info.start_and_end_mz2
+  end
+
+  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
+        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
+    end
+  end
+
+  it_should_behave_like "an msrun with basic, non-spectral information"
+end
+
+describe 'a basic scan info generator', :shared => true do
+
+  def check_table(table, answer)
+    answer.each do |k,v|
+      if v == nil
+        table[k].should be_nil
+      else
+        table[k].should be_close(v, 0.000001)
+      end
+    end
+  end
+  
+  it 'generates precursor_mz_by_scan_num lookup table' do
+    ar = @run.precursor_mz_by_scan_num
+    check_table(ar, @info.num_to_prec_mz_hash)
+  end
+
+  it 'class method -> precursor_mz_by_scan_num (with file)' do
+    ar = @info.klass.precursor_mz_by_scan_num(@info.file) 
+    check_table(ar, @info.num_to_prec_mz_hash)
+  end
+end
+
+MzXML_version_1_info = MyOpenStruct.new do |info|
+  info.file = Tfiles_l + '/yeast_gly_mzXML/000.mzXML'
+  info.klass = MS::MSRun
+  info.filetype = :mzxml
+  info.version = '1.0'
+  info.scan_count = 3748
+  #info.scan_counts = [3748, 937, nil] ## need to get ms2
+  info.start_time = 0.44
+  info.end_time = 5102.55
+  info.num_to_prec_mz_hash = {
+    0 => nil,
+    1 => nil,
+    2 => 391.045410,
+    3 => 446.009033,
+    4 => 1222.033203,
+    5 => nil,
+    6 => 390.947449,
+    3744 => 338.779114,
+    3745 => nil,
+    3746 => 304.136597,
+    3748 => 433.564941,
+  }
+  info.scans = {}
+
+  info.scans[0] = {
+    :num => 1,
+    :ms_level => 1,
+    :time => 0.440,
+  }
+  info.scans[1] = {
+    :num => 2,
+    :ms_level => 2,
+    :time => 1.90,
+    :precursors => [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)]
+  }
+  info.scan_count0 = info.scan_count
+  info.scan_count1 = 937
+  info.scan_count2 = 2811
+  info.start_and_end_mz1 = [300.0, 1500.0]
+  info.start_and_end_mz2 = [0.0, 2000.0]
+end
+
+describe MS::MSRun, "on mzXML version 1 files (w/o spectra)" do
+  spec_large do
+    before(:all) do
+      @info = MzXML_version_1_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
+    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 mzXML version 1 files (w/spectra)" do
+  spec_large do
+    before(:all) do
+      @info = MzXML_version_1_info
+      start = Time.now
+      @run = @info.klass.new(@info.file)
+      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 '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.klass = MS::MSRun
+  info.filetype = :mzxml
+  info.version = '2.0'
+  info.scan_count = 3620
+  #info.scan_counts = ??
+  info.start_time = 0.13
+  info.end_time = 5099.69
+  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,
+  }
+  info.scans = {}
+  info.scans[0]= {
+    :num => 1,
+    :ms_level => 1,
+    :time => 0.13,
+  }
+  info.scans[1] = {
+    :num => 2,
+    :ms_level => 2,
+    :time => 1.49,
+    :precursors => [MS::Precursor.new(:mz => 390.9291992, :intensity => 8.14409e+006)]
+  }
+  info.scans[-1] = {
+    :num => 3620,
+    :ms_level => 2,
+    :time => 5099.69,
+    :precursors => [MS::Precursor.new(:mz => 357.0411987, :intensity => 643017.0)]
+  }
+  info.scan_count0 = info.scan_count
+  info.scan_count1 = 905
+  info.scan_count2 = 2715
+  info.start_and_end_mz1 = [300.0, 1500.0]
+  # 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] 
+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
+
+    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 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
+
+    it_should_behave_like "an msrun with spectrum"
+    it_should_behave_like 'a basic scan info generator'
+  end
+end
+
+Mzdata_105_info = MyOpenStruct.new do |info|
+  info.file = Tfiles_l + '/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
+  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.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, Bioworks 3.3 is broken
+  }
+
+  info.scans = {}
+  info.scans[0] = {
+    :num => 1,
+    :ms_level => 1,
+    :time => 0.13002,  # a little rounding error coming from minutes
+  }
+  info.scans[1] = {
+    :num => 2,
+    :ms_level => 2,
+    :time => 0.024833 * 60,   # 1.48998
+    :precursors => [MS::Precursor.new( :mz => 390.9291992, :intensity => 8.144094e+006) ],
+  }
+  info.scans[-1] = {
+    :num => 3619,
+    :ms_level => 2,
+    #:time => 5099.69, 
+    :time => 84.968500 * 60,  #   5098.11
+
+    :precursors => [MS::Precursor.new( :mz => 424.853821, :intensity => 738590.0 )] # wrong
+  }
+  info.scan_count0 = info.scan_count
+  info.scan_count1 = 905
+  info.scan_count2 = 2714  # should be 2715, they dropped the last scan!
+  info.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]
+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
+
+    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
+
+    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
+      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] 
+
+        precursor = scan.precursors.first
+        precursor.mz.should be_close(exp_mz, 0.00001)
+        precursor.intensity.should be_close(exp_int, 51)
+
+        prec_mz_cnt += 1
+      end
+  end
+end
+end
+
+describe MS::MSRun, 'with small file of twenty scans' do
+  before(:each) 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)
+    end
+  end
+end
+
+describe MS::MSRun, 'with a small set of scans' do 
+  it 'can add parent scans' do
+    vals = [
+      [1,1,0.13], 
+      [2,2,0.23], 
+      [3,2,0.33], 
+      [4,3,0.43], 
+      [5,3,0.53], 
+      [6,1,0.63], 
+      [7,2,0.73], 
+      [8,3,0.83], 
+      [9,2,0.93]
+    ]
+    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
+    end
+    scans.size.should == vals.size
+    s = scans
+    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]
+    end
+  end
+end
+
+=begin
+###################################################
+# SHOULD IMPLEMENT BASIC INFO FOR ALL FILE TYPES
+###################################################
+
+require 'test/unit'
+require 'ms/mzxml/parser'
+
+class MSMzXML < Test::Unit::TestCase
+  def initialize(arg)
+    super(arg)
+    @tfiles = File.dirname(__FILE__) + '/tfiles/'
+    @tscans = @tfiles + "opd1/twenty_scans.mzXML"
+    @big_file = "../bioworks2prophet/xml/opd00001_test_set/opd00001_prophprepped/000.mzXML"
+  end
+
+  def test_basic_info
+    hash = MS::MzXML::Parser.new.basic_info(@tscans)
+    assert_equal({:scan_count=>[20, 5, 15], :start_time=>0.44, :end_time=>27.05, :start_mz=>300.0, :end_mz=>1500.0, :ms_level=>1}, hash, "basic info the same")
+  end
+
+end
+
+=end
+
+

data/specs/ms/parser_spec.rb

@@ -0,0 +1,92 @@
+
+require File.expand_path( File.dirname(__FILE__) + '/../spec_helper' )
+require 'ms/parser'
+
+describe "a MS::Parser on a file", :shared => true do 
+  it 'finds filetype and version on file and handle' do
+    ft_version = nil
+    File.open(@file) do |fh|
+      ft_version = MS::Parser.filetype_and_version(fh)
+    end
+    ft_version.should == @filetype_version
+    ft_version = MS::Parser.filetype_and_version(@file)
+    ft_version.should == @filetype_version
+  end
+
+  it 'creates a sub-classed parser responding to "msrun"' do
+    parser = MS::Parser.new(@file, :msrun) 
+    parser.class.to_s.should match(/^MS::Parser::/)
+    parser.class.to_s.should match(Regexp.new(Regexp.escape(@subclass)))
+    parser.respond_to?(:msrun).should be_true
+  end
+
+  ########################################################################
+  # NOTE: methods to verify parsing of information should be defined where
+  # that information is require.
+  # 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.
+  ########################################################################
+
+end
+
+describe MS::Parser, "on a RAW file (Xcalibur 1.3 SP 1)" do
+  spec_large do
+    before(:all) do
+      @filetype = :raw
+      @version = nil
+      @filetype_version = [@filetype, @version]
+      @file = Tfiles_large + '/opd1_2runs_2mods/data/020.RAW'
+    end
+
+    it 'finds filetype (NO version yet!) on file and handle' do
+      ft_version = nil
+      File.open(@file) do |fh|
+        ft_version = MS::Parser.filetype_and_version(fh)
+      end
+      ft_version.should == @filetype_version
+      ft_version = MS::Parser.filetype_and_version(@file)
+      ft_version.should == @filetype_version
+    end
+  end
+end
+
+describe MS::Parser, "on an mzXML version 1 file" do
+  spec_large do
+    before(:all) do
+      @filetype = :mzxml
+      @version = '1.0'
+      @filetype_version = [@filetype, @version]
+      @subclass = 'MS::Parser::MzXML'
+      @file = Tfiles_large + '/yeast_gly_mzXML/000.mzXML' 
+    end
+    it_should_behave_like "a MS::Parser on a file"
+  end
+end
+
+describe MS::Parser, "on an mzXML version 2 file" do
+  spec_large do
+    before(:all) do
+      @filetype = :mzxml
+      @version = '2.0'
+      @filetype_version = [@filetype, @version]
+      @subclass = 'MS::Parser::MzXML'
+      @file = Tfiles_large + '/opd1_2runs_2mods/data/020.readw.mzXML'
+    end
+    it_should_behave_like "a MS::Parser on a file"
+  end
+end
+
+describe MS::Parser, "on an mzData version 1.05 file" do
+  spec_large do
+    before(:all) do
+      @filetype = :mzdata
+      @version = '1.05'
+      @filetype_version = [@filetype, @version]
+      @subclass = 'MS::Parser::MzData'
+      @file = Tfiles_large + '/opd1_2runs_2mods/data/020.mzData.xml'
+    end
+    it_should_behave_like "a MS::Parser on a file"
+  end
+end
+