ms-msrun 0.1.0 → 0.2.0

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Files changed (42) hide show
  1. data/.gitignore +3 -0
  2. data/.gitmodules +3 -0
  3. data/History +18 -0
  4. data/{README → README.rdoc} +0 -0
  5. data/Rakefile +93 -107
  6. data/VERSION +1 -0
  7. data/lib/lmat.rb +141 -39
  8. data/lib/ms/msrun/nokogiri.rb +1 -0
  9. data/lib/ms/msrun/search_dev_notes.txt +47 -0
  10. data/spec/lmat_spec.rb +87 -11
  11. data/spec/metadata/opd1/000.v1.mzXML.yml +3 -0
  12. data/spec/metadata/opd1/000.v2.1.mzXML.yml +3 -0
  13. data/spec/metadata/opd1/020.mzData.xml.yml +3 -0
  14. data/spec/metadata/opd1/020.v2.0.readw.mzXML.yml +3 -0
  15. data/spec/ms/msrun/hpricot.rb +38 -0
  16. data/spec/ms/msrun/index_spec.rb +12 -13
  17. data/spec/ms/msrun/search_spec.rb +5 -4
  18. data/spec/ms/msrun/sha1_spec.rb +3 -6
  19. data/spec/ms/msrun/test_parsing_xml_frags/parse_test.rb +25 -0
  20. data/spec/ms/msrun/test_parsing_xml_frags/test1.xml +5 -0
  21. data/spec/ms/msrun/test_parsing_xml_frags/test2.xml +6 -0
  22. data/spec/ms/msrun/test_parsing_xml_frags/test3.xml +4 -0
  23. data/spec/ms/msrun/test_parsing_xml_frags/test4.xml +11 -0
  24. data/spec/ms/msrun/test_parsing_xml_frags/test_failures.rb +47 -0
  25. data/spec/ms/msrun_bm.rb +22 -0
  26. data/spec/ms/msrun_spec.rb +90 -109
  27. data/spec/ms/scan_spec.rb +5 -6
  28. data/spec/ms/spectrum/compare_spec.rb +31 -28
  29. data/spec/ms/spectrum/filter_spec.rb +15 -13
  30. data/spec/spec_helper.rb +21 -0
  31. data/spec/testfiles/lmat/tmp1.lmat +0 -0
  32. data/spec/testfiles/lmat/tmp1.lmata +44 -0
  33. data/spec/testfiles/lmat/tmp2.lmata +11 -0
  34. data/spec/testfiles/opd1/000.v1.mzXML +418 -0
  35. data/spec/testfiles/opd1/000.v1.mzXML.key.yml +51 -0
  36. data/spec/testfiles/opd1/000.v2.1.mzXML +382 -0
  37. data/spec/testfiles/opd1/000.v2.1.mzXML.key.yml +51 -0
  38. data/spec/testfiles/opd1/020.mzData.xml +683 -0
  39. data/spec/testfiles/opd1/020.mzData.xml.key.yml +43 -0
  40. data/spec/testfiles/opd1/020.v2.0.readw.mzXML +382 -0
  41. data/spec/testfiles/opd1/020.v2.0.readw.mzXML.key.yml +46 -0
  42. metadata +85 -34
@@ -0,0 +1,683 @@
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+ <?xml version="1.0" encoding="UTF-8"?>
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+ <mzData version="1.05" accessionNumber="psi-ms:12345" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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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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+ <data precision="64" endian="little" 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+ </mzArrayBinary>
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+ <intenArrayBinary>
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+ <cvParam cvLabel="psi" accession="PSI:1000041" name="ChargeState" value="3"/>
413
+ </ionSelection>
414
+ <activation>
415
+ <cvParam cvLabel="psi" accession="PSI:1000044" name="Method" value="CID"/>
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+ <cvParam cvLabel="psi" accession="PSI:1000045" name="CollisionEnergy" value="35.00"/>
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+ </activation>
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+ </precursor>
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+ </precursorList>
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+ </spectrumDesc>
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+ <mzArrayBinary>
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+ </intenArrayBinary>
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+ </spectrum>
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+ <spectrum id="13">
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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="13"/>
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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"/>
436
+ <cvParam cvLabel="psi" accession="PSI:1000037" name="Polarity" value="positive"/>
437
+ <cvParam cvLabel="psi" accession="PSI:1000038" name="TimeInMinutes" value="0.288833"/>
438
+ <cvParam cvLabel="psi" accession="PSI:1000035" name="PeakProcessing" value="continuous"/>
439
+ <cvParam cvLabel="tmo" accession="TMO:1000001" name="Filter" value="+ c Full ms [300.00-1500.00]"/>
440
+ </spectrumInstrument>
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+ </spectrumSettings>
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+ </spectrumDesc>
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+ <mzArrayBinary>
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+ <precursorList count = "1">
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+ <precursor msLevel="2" spectrumRef="19">
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+ <ionSelection>
664
+ <cvParam cvLabel="psi" accession="PSI:1000040" name="MassToChargeRatio" value="361.671875"/>
665
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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>
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+ </spectrumDesc>
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+ </intenArrayBinary>
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+ </spectrum>
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+ </spectrumList>
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+ </mzData>