ms-sequest 0.0.11 → 0.0.12

data/spec/ms/sequest/sqt_spec.rb

@@ -0,0 +1,78 @@
+require File.expand_path( File.dirname(__FILE__) + '/../../spec_helper' )
+
+require File.dirname(__FILE__) + '/sqt_spec_helper'
+
+require 'ms/sequest/sqt'
+
+describe 'reading a small sqt file' do
+
+  before do
+    file = TESTFILES + '/small.sqt'
+    @sqt = Ms::Sequest::Sqt.new(file)
+  end
+
+  it 'can access header entries like a hash' do
+    header = @sqt.header
+    HeaderHash.each do |k,v|
+      header[k].is v
+    end
+  end
+
+  it 'can access header entries with methods' do
+    header = @sqt.header
+    # for example:
+    header.database.is HeaderHash['Database']
+    # all working:
+    HeaderHash.each do |k,v|
+      header.send(Ms::Sequest::Sqt::Header::KeysToAtts[k]).is v
+    end
+
+  end
+
+  it 'has spectra, matches, and loci' do
+    svt = @sqt.spectra[16]
+    reply = {:first => @sqt.spectra.first, :last => @sqt.spectra.last, :seventeenth => svt, :first_match_17 => svt.matches.first, :last_match_17 => svt.matches.last, :last_match_17_last_loci => svt.matches.last.loci.last}
+    [:first, :last, :seventeenth, :first_match_17, :last_match_17, :last_match_17_last_loci].each do |key|
+      TestSpectra[key].each do |k,v|
+        if v.is_a? Float
+          reply[key].send(k).should.be.close(v, 0.0000000001)
+        else
+          next if key == :last_match_17_last_loci
+          #p k
+          #p v
+          reply[key].send(k).is v
+        end
+      end
+    end
+    @sqt.spectra[16].matches.first.loci.size.is 1
+    @sqt.spectra[16].matches.last.loci.size.is 1
+  end
+
+end
+
+#class SqtGroup_ReadingFiles < MiniTest::Spec
+  #before(:each) do
+    #file1 = TESTFILES + '/small.sqt'
+    #file2 = TESTFILES + '/small2.sqt'
+    #@sqg = Ms::Sequest::SqtGroup.new([file1, file2])
+  #end
+
+  #it 'has peptide hits' do
+    #peps = @sqg.peps
+    #peps.size.is 86
+    ## first hit in 020
+    #peps.first.sequence.is 'R.Y#RLGGS#T#K.K'
+    #peps.first.base_name.is 'small'
+    ## last hit in 040
+    #peps.last.sequence.is 'K.T#IS#S#QK.K'
+    #peps.last.base_name.is 'small2'
+  #end
+
+  #it 'has prots' do
+    ### FROZEN:
+    #@sqg.prots.size.is 72
+    #sorted = @sqg.prots.sort_by {|v| v.reference }
+    #sorted.first.reference.is 'gi|16127996|ref|NP_414543.1|'
+    #sorted.first.peps.size.is 33
+  #end
+#end

data/spec/ms/sequest/sqt_spec_helper.rb

@@ -0,0 +1,34 @@
+
+
+HeaderHash = {}
+header_doublets = [
+  %w(SQTGenerator	mspire),
+  %w(SQTGeneratorVersion	0.3.1),
+  %w(Database	C:\Xcalibur\database\ecoli_K12_ncbi_20060321.fasta),
+  %w(FragmentMasses	AVG),
+  %w(PrecursorMasses	AVG),
+  ['StartTime', ''],
+  ['Alg-MSModel', 'LCQ Deca XP'],
+  %w(DBLocusCount	4237),
+  %w(Alg-FragMassTol	1.0000),
+  %w(Alg-PreMassTol	25.0000),
+  ['Alg-IonSeries', '0 1 1 0.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 0.0'],
+  %w(Alg-PreMassUnits	ppm),
+  ['Alg-Enzyme', 'Trypsin(KR/P) (2)'],
+
+  ['Comment', ['ultra small file created for testing', 'Created from Bioworks .srf file']],
+  ['DynamicMod', ['M*=+15.99940', 'STY#=+79.97990']],
+  ['StaticMod', []],
+].each do |double|
+  HeaderHash[double[0]] = double[1]
+end
+
+TestSpectra = {
+  :first => { :first_scan=>2, :last_scan=>2, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>390.92919921875, :total_intensity=>2653.90307617188, :lowest_sp=>0.0, :num_matched_peptides=>0, :matches=>[]},
+  :last => { :first_scan=>27, :last_scan=>27, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>393.008056640625, :total_intensity=>2896.16967773438, :lowest_sp=>0.0, :num_matched_peptides=>0, :matches=>[] },
+  :seventeenth => {:first_scan=>23, :last_scan=>23, :charge=>1, :time_to_process=>0.0, :node=>"TESLA", :mh=>1022.10571289062, :total_intensity=>3637.86059570312, :lowest_sp=>0.0, :num_matched_peptides=>41},
+  :first_match_17 => { :rxcorr=>1, :rsp=>5, :mh=>1022.11662242, :deltacn_orig=>0.0, :xcorr=>0.725152492523193, :sp=>73.9527359008789, :ions_matched=>6, :ions_total=>24, :sequence=>"-.MGT#TTM*GVK.L", :manual_validation_status=>"U", :first_scan=>23, :last_scan=>23, :charge=>1, :deltacn=>0.0672458708286285, :aaseq => 'MGTTTMGVK' },
+  :last_match_17 => {:rxcorr=>10, :rsp=>16, :mh=>1022.09807242, :deltacn_orig=>0.398330867290497, :xcorr=>0.436301857233047, :sp=>49.735767364502, :ions_matched=>5, :ions_total=>21, :sequence=>"-.MRT#TSFAK.V", :manual_validation_status=>"U", :first_scan=>23, :last_scan=>23, :charge=>1, :deltacn=>1.1, :aaseq => 'MRTTSFAK'},
+  :last_match_17_last_loci => {:reference =>'gi|16129390|ref|NP_415948.1|', :first_entry =>'gi|16129390|ref|NP_415948.1|', :locus =>'gi|16129390|ref|NP_415948.1|', :description => 'Fake description' }
+}
+

data/spec/ms/sequest/srf/search_spec.rb

@@ -0,0 +1,53 @@
+require File.expand_path( File.dirname(__FILE__) + '/../../../spec_helper' )
+require File.expand_path( File.dirname(__FILE__) + '/search_spec_helper' )
+
+require 'fileutils'
+
+require 'ms/sequest/srf'
+require 'ms/sequest/srf/search'
+
+describe 'converting a large srf to an ms search format' do
+
+  @file = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.srf'
+  @srf = Ms::Sequest::Srf.new(@file)
+
+  def del(file)
+    if File.exist?(file)
+      if File.directory?(file)
+        FileUtils.rm_rf(file)
+      else
+        File.unlink(file)
+      end
+    end
+  end
+
+  it 'converts to mgf' do
+    @output = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.mgf.tmp'
+    @srf.to_mgf(@output)
+    ok File.exist?(@output)
+    output = IO.read(@output)
+    # tests are just frozen right now, not checked for accuracy
+    ok output.include?(SRF_TO_MGF_HELPER::FIRST_MSMS)
+    ok output[1000..-1].include?(SRF_TO_MGF_HELPER::LAST_MSMS)
+    del(@output)
+  end
+
+  it 'generates .dta files' do
+    @output = Ms::TESTDATA + '/sequest/opd1_static_diff_mods/000.dta.tmp'
+    @srf.to_dta(@output)
+    ok File.exist?(@output)
+    ok File.directory?(@output)
+    # frozen (not verified):
+    Dir[@output + "/*.*"].size.is 3893 # the correct number files
+
+    first_file = @output + '/000.2.2.1.dta'
+    ok File.exist?(first_file) 
+    IO.read(first_file).is SRF_TO_DTA_HELPER::FIRST_SCAN.gsub("\n", "\r\n")
+    last_file = @output + '/000.3748.3748.3.dta'
+    IO.read(last_file).is SRF_TO_DTA_HELPER::LAST_SCAN.gsub("\n", "\r\n")
+
+    del(@output)
+  end
+
+end
+

data/spec/ms/sequest/srf/search_spec_helper.rb

@@ -0,0 +1,341 @@
+class SRF_TO_MGF_HELPER
+  FIRST_MSMS = <<FINISH
+BEGIN IONS
+TITLE=000.2.2.1.dta
+CHARGE=1+
+PEPMASS=391.04541015625
+111.976043701172 41418.0
+112.733383178711 88292.0
+113.536590576172 26129.0
+149.049530029297 2852380.0
+149.960266113281 110104.0
+150.578399658203 4607.0
+155.026885986328 16524.0
+160.48388671875 17154.0
+161.9013671875 6562.0
+164.386596679688 76498.0
+166.8427734375 1663866.0
+167.719482421875 72010.0
+168.693237304688 57081.0
+197.131774902344 7933.0
+217.975738525391 20193.0
+218.799468994141 15350.0
+222.215576171875 21254.0
+223.027404785156 27495.0
+224.90771484375 16117.0
+225.895538330078 25061.0
+253.583435058594 7431.0
+255.372528076172 25846.0
+257.151245117188 5435.0
+258.856323242188 26408.0
+260.166259765625 261245.0
+260.812072753906 639646.0
+261.715698242188 82724.0
+262.366638183594 4.0
+272.052124023438 43365.0
+277.773315429688 159994.0
+278.856872558594 2140713.0
+279.935546875 397598.0
+280.699951171875 4.0
+289.641723632812 32978.0
+290.385864257812 31836.0
+291.786682128906 15850.0
+296.626831054688 54212.0
+298.6279296875 22051.0
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+301.489501953125 10696.0
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+407.412780761719 18959.0
+781.085327148438 10104.0
+END IONS
+
+FINISH
+
+LAST_MSMS = <<FINISH
+BEGIN IONS
+TITLE=000.3748.3748.3.dta
+CHARGE=3+
+PEPMASS=433.56494098625
+143.466918945312 2110.0
+151.173095703125 4134.0
+158.817443847656 2565.0
+178.629333496094 6114.0
+180.065307617188 879.0
+185.164703369141 2364.0
+206.865417480469 7925.0
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+212.763122558594 893.0
+217.749298095703 2202.0
+227.912048339844 4343.0
+235.973571777344 2485.0
+236.941436767578 679.0
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+271.46435546875 1504.0
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+278.331237792969 775.0
+282.728149414062 963.0
+287.679931640625 1749.0
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+299.569091796875 5620.0
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+308.79541015625 3738.0
+312.496154785156 3964.0
+313.62890625 11383.0
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+326.534423828125 4564.0
+331.253601074219 7761.0
+334.9482421875 4798.0
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+338.891174316406 5830.0
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+378.099853515625 11617.0
+378.795227050781 1641.0
+380.755065917969 7448.0
+386.034118652344 12462.0
+389.507751464844 15551.0
+390.844665527344 10268.0
+391.481140136719 500.0
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+396.465515136719 3636.0
+397.885864257812 1616.0
+400.766723632812 1113.0
+403.266967773438 8535.0
+404.394714355469 1578.0
+406.269592285156 7361.0
+407.214721679688 919.0
+408.305969238281 11683.0
+409.64501953125 14506.0
+410.707946777344 6735.0
+411.557250976562 6330.0
+414.049255371094 2606.0
+414.9775390625 25274.0
+415.742065429688 5809.0
+418.659118652344 2842.0
+420.640441894531 4050.0
+421.357604980469 4565.0
+424.955871582031 4801.0
+425.623840332031 1578.0
+427.966552734375 5836.0
+431.106018066406 4433.0
+431.956970214844 2428.0
+432.5595703125 7390.0
+433.419677734375 2093.0
+441.233154296875 3196.0
+441.985717773438 2048.0
+448.181823730469 3643.0
+449.430480957031 11621.0
+450.174560546875 4437.0
+450.84521484375 3907.0
+451.573608398438 6557.0
+452.447204589844 1461.0
+453.993347167969 3555.0
+465.704284667969 6213.0
+466.320739746094 1146.0
+468.420104980469 3492.0
+482.678771972656 3357.0
+610.4111328125 8968.0
+END IONS
+FINISH
+end
+
+# these have been checked against Bioworks .dta output
+class SRF_TO_DTA_HELPER
+  FIRST_SCAN = <<FINISH
+391.045410 1
+111.9760 41418
+112.7334 88292
+113.5366 26129
+149.0495 2852380
+149.9603 110104
+150.5784 4607
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+262.3666 4
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+374.6720 70584
+388.6606 22746
+405.4440 23893
+406.4814 27502
+407.4128 18959
+781.0853 10104
+FINISH
+
+LAST_SCAN = <<FINISH
+1298.680271 3
+143.4669 2110
+151.1731 4134
+158.8174 2565
+178.6293 6114
+180.0653 879
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+433.4197 2093
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+610.4111 8968
+FINISH
+end