ms-msrun 0.1.0 → 0.2.0
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- data/.gitignore +3 -0
- data/.gitmodules +3 -0
- data/History +18 -0
- data/{README → README.rdoc} +0 -0
- data/Rakefile +93 -107
- data/VERSION +1 -0
- data/lib/lmat.rb +141 -39
- data/lib/ms/msrun/nokogiri.rb +1 -0
- data/lib/ms/msrun/search_dev_notes.txt +47 -0
- data/spec/lmat_spec.rb +87 -11
- data/spec/metadata/opd1/000.v1.mzXML.yml +3 -0
- data/spec/metadata/opd1/000.v2.1.mzXML.yml +3 -0
- data/spec/metadata/opd1/020.mzData.xml.yml +3 -0
- data/spec/metadata/opd1/020.v2.0.readw.mzXML.yml +3 -0
- data/spec/ms/msrun/hpricot.rb +38 -0
- data/spec/ms/msrun/index_spec.rb +12 -13
- data/spec/ms/msrun/search_spec.rb +5 -4
- data/spec/ms/msrun/sha1_spec.rb +3 -6
- data/spec/ms/msrun/test_parsing_xml_frags/parse_test.rb +25 -0
- data/spec/ms/msrun/test_parsing_xml_frags/test1.xml +5 -0
- data/spec/ms/msrun/test_parsing_xml_frags/test2.xml +6 -0
- data/spec/ms/msrun/test_parsing_xml_frags/test3.xml +4 -0
- data/spec/ms/msrun/test_parsing_xml_frags/test4.xml +11 -0
- data/spec/ms/msrun/test_parsing_xml_frags/test_failures.rb +47 -0
- data/spec/ms/msrun_bm.rb +22 -0
- data/spec/ms/msrun_spec.rb +90 -109
- data/spec/ms/scan_spec.rb +5 -6
- data/spec/ms/spectrum/compare_spec.rb +31 -28
- data/spec/ms/spectrum/filter_spec.rb +15 -13
- data/spec/spec_helper.rb +21 -0
- data/spec/testfiles/lmat/tmp1.lmat +0 -0
- data/spec/testfiles/lmat/tmp1.lmata +44 -0
- data/spec/testfiles/lmat/tmp2.lmata +11 -0
- data/spec/testfiles/opd1/000.v1.mzXML +418 -0
- data/spec/testfiles/opd1/000.v1.mzXML.key.yml +51 -0
- data/spec/testfiles/opd1/000.v2.1.mzXML +382 -0
- data/spec/testfiles/opd1/000.v2.1.mzXML.key.yml +51 -0
- data/spec/testfiles/opd1/020.mzData.xml +683 -0
- data/spec/testfiles/opd1/020.mzData.xml.key.yml +43 -0
- data/spec/testfiles/opd1/020.v2.0.readw.mzXML +382 -0
- data/spec/testfiles/opd1/020.v2.0.readw.mzXML.key.yml +46 -0
- metadata +85 -34
@@ -0,0 +1,683 @@
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<?xml version="1.0" encoding="UTF-8"?>
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<description>
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<admin>
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<sampleName>E_coli03</sampleName>
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<sampleDescription></sampleDescription>
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<sourceFile>
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<nameOfFile>020.raw</nameOfFile>
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<pathToFile>file://C:/Xcalibur/data/john/opd1_2runs_2mods</pathToFile>
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<fileType>2.0</fileType>
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</sourceFile>
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<contact>
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<name></name>
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<institution></institution>
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<contactInfo></contactInfo>
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</contact>
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</admin>
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<instrument>
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<instrumentName>LCQ Deca XP</instrumentName>
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<source>
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<cvParam cvLabel="psi" accession="PSI:1000008" name="IonizationType" value=""/>
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</source>
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<analyzerList count="0">
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<analyzer>
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<cvParam cvLabel="psi" accession="PSI:1000010" name="AnalyzerType" value="PaulTrap"/>
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<cvParam cvLabel="psi" accession="PSI:1000011" name="Resolution" value="0"/>
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<cvParam cvLabel="psi" accession="PSI:1000012" name="Accuracy" value="0.5000"/>
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</analyzer>
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</analyzerList>
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<detector>
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<cvParam cvLabel="psi" accession="PSI:1000026" name="DetectorType" value="EM"/>
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</detector>
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</instrument>
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<dataProcessing>
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<software>
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<name>Bioworks Browser</name>
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<version>3.3</version>
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</software>
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<processingMethod>
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<cvParam cvLabel="psi" accession="PSI:1000033" name="Deisotoping" value="false"/>
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<cvParam cvLabel="psi" accession="PSI:1000034" name="ChargeDeconvolutionW" value="false"/>
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<cvParam cvLabel="psi" accession="PSI:1000035" name="PeakProcessing" value="discrete"/>
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</processingMethod>
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</dataProcessing>
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</description>
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<spectrumList count="2715">
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<spectrum id="1">
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<spectrumDesc>
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<spectrumSettings>
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<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
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<acquisition acqNumber="1"/>
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</acqSpecification>
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<spectrumInstrument msLevel="1" mzRangeStart="300.000000" mzRangeStop="1500.000000">
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<cvParam cvLabel="psi" accession="PSI:1000036" name="ScanMode" value="MassScan"/>
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<cvParam cvLabel="psi" accession="PSI:1000037" name="Polarity" value="positive"/>
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<cvParam cvLabel="psi" accession="PSI:1000038" name="TimeInMinutes" value="0.002167"/>
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<cvParam cvLabel="psi" accession="PSI:1000035" name="PeakProcessing" value="continuous"/>
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<cvParam cvLabel="tmo" accession="TMO:1000001" name="Filter" value="+ c Full ms [300.00-1500.00]"/>
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</spectrumInstrument>
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</spectrumSettings>
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</spectrumDesc>
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<mzArrayBinary>
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<cvParam cvLabel="psi" accession="PSI:1000041" name="ChargeState" value="3"/>
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159
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</ionSelection>
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160
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<activation>
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161
|
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<cvParam cvLabel="psi" accession="PSI:1000044" name="Method" value="CID"/>
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162
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<cvParam cvLabel="psi" accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
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163
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</activation>
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164
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+
</precursor>
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165
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</precursorList>
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166
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174
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+
<spectrum id="5">
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175
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<spectrumDesc>
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176
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<spectrumSettings>
|
177
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<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
|
178
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<acquisition acqNumber="5"/>
|
179
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</acqSpecification>
|
180
|
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<spectrumInstrument msLevel="1" mzRangeStart="300.000000" mzRangeStop="1500.000000">
|
181
|
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<cvParam cvLabel="psi" accession="PSI:1000036" name="ScanMode" value="MassScan"/>
|
182
|
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<cvParam cvLabel="psi" accession="PSI:1000037" name="Polarity" value="positive"/>
|
183
|
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<cvParam cvLabel="psi" accession="PSI:1000038" name="TimeInMinutes" value="0.089667"/>
|
184
|
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<cvParam cvLabel="psi" accession="PSI:1000035" name="PeakProcessing" value="continuous"/>
|
185
|
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<cvParam cvLabel="tmo" accession="TMO:1000001" name="Filter" value="+ c Full ms [300.00-1500.00]"/>
|
186
|
+
</spectrumInstrument>
|
187
|
+
</spectrumSettings>
|
188
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</spectrumDesc>
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189
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|
448
|
+
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|
449
|
+
</spectrum>
|
450
|
+
<spectrum id="14">
|
451
|
+
<spectrumDesc>
|
452
|
+
<spectrumSettings>
|
453
|
+
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
|
454
|
+
<acquisition acqNumber="14"/>
|
455
|
+
</acqSpecification>
|
456
|
+
<spectrumInstrument msLevel="2" mzRangeStart="90.000000" mzRangeStop="755.000000">
|
457
|
+
<cvParam cvLabel="psi" accession="PSI:1000036" name="ScanMode" value="MassScan"/>
|
458
|
+
<cvParam cvLabel="psi" accession="PSI:1000037" name="Polarity" value="positive"/>
|
459
|
+
<cvParam cvLabel="psi" accession="PSI:1000038" name="TimeInMinutes" value="0.312667"/>
|
460
|
+
<cvParam cvLabel="psi" accession="PSI:1000035" name="PeakProcessing" value="continuous"/>
|
461
|
+
<cvParam cvLabel="tmo" accession="TMO:1000001" name="Filter" value="+ c d Full ms2 371.04@cid35.00 [90.00-755.00]"/>
|
462
|
+
</spectrumInstrument>
|
463
|
+
</spectrumSettings>
|
464
|
+
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|
465
|
+
<precursor msLevel="2" spectrumRef="13">
|
466
|
+
<ionSelection>
|
467
|
+
<cvParam cvLabel="psi" accession="PSI:1000040" name="MassToChargeRatio" value="371.043518"/>
|
468
|
+
<cvParam cvLabel="psi" accession="PSI:1000041" name="ChargeState" value="2"/>
|
469
|
+
<cvParam cvLabel="psi" accession="PSI:1000041" name="ChargeState" value="3"/>
|
470
|
+
</ionSelection>
|
471
|
+
<activation>
|
472
|
+
<cvParam cvLabel="psi" accession="PSI:1000044" name="Method" value="CID"/>
|
473
|
+
<cvParam cvLabel="psi" accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
|
474
|
+
</activation>
|
475
|
+
</precursor>
|
476
|
+
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|
477
|
+
</spectrumDesc>
|
478
|
+
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|
479
|
+
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|
480
|
+
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|
481
|
+
<intenArrayBinary>
|
482
|
+
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|
483
|
+
</intenArrayBinary>
|
484
|
+
</spectrum>
|
485
|
+
<spectrum id="15">
|
486
|
+
<spectrumDesc>
|
487
|
+
<spectrumSettings>
|
488
|
+
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
|
489
|
+
<acquisition acqNumber="15"/>
|
490
|
+
</acqSpecification>
|
491
|
+
<spectrumInstrument msLevel="2" mzRangeStart="100.000000" mzRangeStop="830.000000">
|
492
|
+
<cvParam cvLabel="psi" accession="PSI:1000036" name="ScanMode" value="MassScan"/>
|
493
|
+
<cvParam cvLabel="psi" accession="PSI:1000037" name="Polarity" value="positive"/>
|
494
|
+
<cvParam cvLabel="psi" accession="PSI:1000038" name="TimeInMinutes" value="0.338333"/>
|
495
|
+
<cvParam cvLabel="psi" accession="PSI:1000035" name="PeakProcessing" value="continuous"/>
|
496
|
+
<cvParam cvLabel="tmo" accession="TMO:1000001" name="Filter" value="+ c d Full ms2 407.59@cid35.00 [100.00-830.00]"/>
|
497
|
+
</spectrumInstrument>
|
498
|
+
</spectrumSettings>
|
499
|
+
<precursorList count = "1">
|
500
|
+
<precursor msLevel="2" spectrumRef="14">
|
501
|
+
<ionSelection>
|
502
|
+
<cvParam cvLabel="psi" accession="PSI:1000040" name="MassToChargeRatio" value="407.593689"/>
|
503
|
+
<cvParam cvLabel="psi" accession="PSI:1000041" name="ChargeState" value="2"/>
|
504
|
+
<cvParam cvLabel="psi" accession="PSI:1000041" name="ChargeState" value="3"/>
|
505
|
+
</ionSelection>
|
506
|
+
<activation>
|
507
|
+
<cvParam cvLabel="psi" accession="PSI:1000044" name="Method" value="CID"/>
|
508
|
+
<cvParam cvLabel="psi" accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
|
509
|
+
</activation>
|
510
|
+
</precursor>
|
511
|
+
</precursorList>
|
512
|
+
</spectrumDesc>
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<data precision="64" endian="little" length="74">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</data>
|
645
|
+
</intenArrayBinary>
|
646
|
+
</spectrum>
|
647
|
+
<spectrum id="20">
|
648
|
+
<spectrumDesc>
|
649
|
+
<spectrumSettings>
|
650
|
+
<acqSpecification spectrumType="discrete" methodOfCombination="sum" count="1">
|
651
|
+
<acquisition acqNumber="20"/>
|
652
|
+
</acqSpecification>
|
653
|
+
<spectrumInstrument msLevel="2" mzRangeStart="85.000000" mzRangeStop="735.000000">
|
654
|
+
<cvParam cvLabel="psi" accession="PSI:1000036" name="ScanMode" value="MassScan"/>
|
655
|
+
<cvParam cvLabel="psi" accession="PSI:1000037" name="Polarity" value="positive"/>
|
656
|
+
<cvParam cvLabel="psi" accession="PSI:1000038" name="TimeInMinutes" value="0.455167"/>
|
657
|
+
<cvParam cvLabel="psi" accession="PSI:1000035" name="PeakProcessing" value="continuous"/>
|
658
|
+
<cvParam cvLabel="tmo" accession="TMO:1000001" name="Filter" value="+ c d Full ms2 361.67@cid35.00 [85.00-735.00]"/>
|
659
|
+
</spectrumInstrument>
|
660
|
+
</spectrumSettings>
|
661
|
+
<precursorList count = "1">
|
662
|
+
<precursor msLevel="2" spectrumRef="19">
|
663
|
+
<ionSelection>
|
664
|
+
<cvParam cvLabel="psi" accession="PSI:1000040" name="MassToChargeRatio" value="361.671875"/>
|
665
|
+
<cvParam cvLabel="psi" accession="PSI:1000041" name="ChargeState" value="2"/>
|
666
|
+
<cvParam cvLabel="psi" accession="PSI:1000041" name="ChargeState" value="3"/>
|
667
|
+
</ionSelection>
|
668
|
+
<activation>
|
669
|
+
<cvParam cvLabel="psi" accession="PSI:1000044" name="Method" value="CID"/>
|
670
|
+
<cvParam cvLabel="psi" accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
|
671
|
+
</activation>
|
672
|
+
</precursor>
|
673
|
+
</precursorList>
|
674
|
+
</spectrumDesc>
|
675
|
+
<mzArrayBinary>
|
676
|
+
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|
677
|
+
</mzArrayBinary>
|
678
|
+
<intenArrayBinary>
|
679
|
+
<data precision="64" endian="little" length="108">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</data>
|
680
|
+
</intenArrayBinary>
|
681
|
+
</spectrum>
|
682
|
+
</spectrumList>
|
683
|
+
</mzData>
|