mspire 0.3.9 → 0.4.2

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Files changed (87) hide show
  1. data/INSTALL +24 -7
  2. data/README +15 -13
  3. data/README.rdoc +18 -0
  4. data/Rakefile +50 -14
  5. data/bin/aafreqs.rb +0 -0
  6. data/bin/bioworks2excel.rb +0 -0
  7. data/bin/bioworks_to_pepxml.rb +2 -1
  8. data/bin/bioworks_to_pepxml_gui.rb +0 -0
  9. data/bin/fasta_shaker.rb +0 -0
  10. data/bin/filter_and_validate.rb +0 -0
  11. data/bin/gi2annot.rb +0 -0
  12. data/bin/id_class_anal.rb +0 -0
  13. data/bin/id_precision.rb +0 -0
  14. data/bin/ms_to_lmat.rb +0 -0
  15. data/bin/pepproph_filter.rb +0 -0
  16. data/bin/protein_summary.rb +0 -0
  17. data/bin/protxml2prots_peps.rb +0 -0
  18. data/bin/raw_to_mzXML.rb +3 -3
  19. data/bin/run_percolator.rb +122 -0
  20. data/bin/sqt_group.rb +0 -0
  21. data/bin/srf_group.rb +0 -0
  22. data/changelog.txt +29 -0
  23. data/lib/ms/gradient_program.rb +0 -1
  24. data/lib/ms/msrun.rb +62 -29
  25. data/lib/ms/parser/mzdata/axml.rb +55 -0
  26. data/lib/ms/parser/mzdata/dom.rb +51 -36
  27. data/lib/ms/parser/mzdata.rb +8 -2
  28. data/lib/ms/parser/mzxml/axml.rb +59 -0
  29. data/lib/ms/parser/mzxml/dom.rb +80 -57
  30. data/lib/ms/parser/mzxml/hpricot.rb +1 -1
  31. data/lib/ms/parser/mzxml/libxml.rb +6 -2
  32. data/lib/ms/parser/mzxml.rb +110 -3
  33. data/lib/ms/parser.rb +4 -4
  34. data/lib/ms/precursor.rb +19 -4
  35. data/lib/ms/scan.rb +7 -7
  36. data/lib/ms/spectrum.rb +249 -58
  37. data/lib/mspire.rb +1 -1
  38. data/lib/spec_id/bioworks.rb +2 -2
  39. data/lib/spec_id/precision/filter/cmdline.rb +8 -1
  40. data/lib/spec_id/precision/prob/cmdline.rb +2 -2
  41. data/lib/spec_id/precision/prob.rb +1 -0
  42. data/lib/spec_id/proph/pep_summary.rb +3 -4
  43. data/lib/spec_id/proph/prot_summary.rb +3 -3
  44. data/lib/spec_id/protein_summary.rb +1 -1
  45. data/lib/spec_id/sequest/pepxml.rb +5 -5
  46. data/lib/spec_id/sqt.rb +4 -4
  47. data/lib/spec_id/srf.rb +49 -8
  48. data/lib/spec_id.rb +5 -0
  49. data/lib/xml_style_parser.rb +16 -2
  50. data/script/compile_and_plot_smriti_final.rb +0 -0
  51. data/script/create_little_pepxml.rb +0 -0
  52. data/script/degenerate_peptides.rb +0 -0
  53. data/script/estimate_fpr_by_cysteine.rb +0 -0
  54. data/script/extract_gradient_programs.rb +1 -1
  55. data/script/find_cysteine_background.rb +0 -0
  56. data/script/genuine_tps_and_probs.rb +0 -0
  57. data/script/get_apex_values_rexml.rb +0 -0
  58. data/script/mascot_fix_pepxml.rb +123 -0
  59. data/script/msvis.rb +0 -0
  60. data/script/mzXML2timeIndex.rb +0 -0
  61. data/script/peps_per_bin.rb +0 -0
  62. data/script/prep_dir.rb +0 -0
  63. data/script/simple_protein_digestion.rb +0 -0
  64. data/script/smriti_final_analysis.rb +0 -0
  65. data/script/sqt_to_meta.rb +0 -0
  66. data/script/top_hit_per_scan.rb +0 -0
  67. data/script/toppred_to_yaml.rb +0 -0
  68. data/script/tpp_installer.rb +0 -0
  69. data/specs/bin/prob_validate_spec.rb +5 -2
  70. data/specs/bin/protein_summary_spec.rb +5 -1
  71. data/specs/ms/msrun_spec.rb +176 -133
  72. data/specs/ms/parser_spec.rb +3 -3
  73. data/specs/ms/spectrum_spec.rb +0 -2
  74. data/specs/spec_id/precision/filter_spec.rb +4 -1
  75. data/specs/spec_id/precision/prob_spec.rb +2 -2
  76. data/specs/spec_id/sequest/pepxml_spec.rb +1 -1
  77. data/specs/spec_id/sqt_spec.rb +5 -5
  78. data/specs/spec_id/srf_spec.rb +56 -93
  79. data/specs/spec_id/srf_spec_helper.rb +121 -284
  80. data/specs/spec_id_spec.rb +3 -0
  81. data/specs/transmem/toppred_spec.rb +1 -0
  82. data/test_files/opd1_2runs_2mods/data/020.mzData.xml +683 -0
  83. data/test_files/opd1_2runs_2mods/data/020.readw.mzXML +382 -0
  84. data/test_files/opd1_2runs_2mods/data/040.mzData.xml +683 -0
  85. data/test_files/opd1_2runs_2mods/data/040.readw.mzXML +382 -0
  86. data/test_files/opd1_2runs_2mods/data/README.txt +6 -0
  87. metadata +247 -229
data/test_files/opd1_2runs_2mods/data/040.mzData.xml ADDED
@@ -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_coli04</sampleName>
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+ <sampleDescription></sampleDescription>
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+ <sourceFile>
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+ <nameOfFile>040.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="2643">
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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="0.002667"/>
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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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+ <intenArrayBinary>
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