ms-msrun 0.1.0 → 0.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
data/spec/testfiles/lmat/tmp1.lmata ADDED
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2xHygOAREgYBkbijgBESEE4QOAAAERIxCRIHoRAREj5wkdLogBESTBoRuVCAERJlAxHKl4AREm8tEd8BABESep4Ry6LAERKKHBITvvAREp4aEdXnwBESq5mSDDLAERK6MhG79YAREsvVEeq5wBES5kWR3CJAERL52BHoSQAREwdaEdXsABETHJSSFIZgERNG9BIAZ1ARE1ZqkcjTgBETaVKSGCxgERODlhHL3AARE5jJkgfHMBETpXgRqzAAERO+95IFsoARE9MaEe3PIBET4xaSN7J4ERPzCxHoP+ARFBdvkhKBcBEUKR4Rui8AERQ/+hISB8ARFEmvkaCbgBEUU8eSLZ34ERRgXxG9J4ARFHHlEdOZABEUf3sSCeEwERSWGBHsqOARFKTOkh+agBEUtJmR6SpAERS+OJAwAAARFMo1kdWNgBEU1VARzjmAERTvehH784ARFQHKkc1GgBEVEb2R7k4gERUiSBHuQEARFTBukacuABEVQhGRw1gAERVPpBHbhgARFXbckYWpABEVgV6RhFYAERWY+JHV2wARFaSvkg6IkBEVzbmR4UrAERXfaJGxPoARFfqjkdLqQBEWBSeRhBYAERYVZRHju0ARFilzEe5ugBEWM9qRr7OAERZDDJIF6nARFk1ZkeJ74BEWWc0SBkvAERZnUBH8cKARFnNekgpHUBEWiAUR80xAERach5Hvm6ARFrOEEfNKoBEWwY6R9+UgERbcrBGWGwARFvOBEiZOWBEXDQSRzNiAERcdIhHs/AARFzHEEgbO8BEXPd2QSAAAERdIBJGB8QARF18gkdO7ABEXbMoSMqRQEReAkZH/WMARF43dkAAAABEXn8eR/fcAERe4epIHaPARF80VEfLCgBEX3XWR3ZLAERfn3ZBAAAARF/lkkfNkIBEYBVUQIAAAERgQI5HlFyARGCL8EfJaoBEYQNAR/RrgERhN7pHlz2ARGGEaEexqwBEYbcgR1nbAERh5fJIL4mARGImjEeBLIBEYqI2RxmGAERjOi5HorUARGN2hEcLQABEY8XsSIXLAERkFVZGWEgARGRmlkf/NgBEZLmIR+tpAERlCepGdewARGVEMkcbAABEZXF4RgOAAERluoBE62AARGX8QkgqisBEZnsKSNEwYERm9iBIDHHARGcqXEfcYwBEZ41oR/ejAERn0IJHq2MARGg4rEcjhwBEaF9URpQsAERokNJHppSARGjgTEbTjABEaRVWSCRKQERpP8JGtFAARGmG1EgSVUBEadSQSA7DQERqDhxGHQgARGplHEhw70BEaqmYSF/sgERq79BHsV2ARGsnSkXvYABEa1mmRpuUAERrjYZHYs8ARGwSMkhl9oBEbEoKSCYKAERsrHpIKA3ARGzegkgD/QBEbRNcR+xWgERtYNpH9xCARG2wyEfxyoBEbfQMRfrYAERuTmZH9BOARG6TQEZ0dABEbwFER0J8AERvSkBHRB0ARG+ZfEa0BgBEb8bYSBaQwERwIOJHhsEARHBHdEaJGgBEcKF2SHLiwERw4mBHJ4QARHGVqkZPQABEceAySBTQgERyI1hHL5UARHJJwEFgAABEcqTWRya4AERzEYJHW0gARHOFyEf/rgBEc/OOR1WoAER0f/hIJ0jARHS7jEbvPABEdOQmRuQAAER1HsBGMxAARHWDhkkLxwBEdcRaSAabQER2BNpHm1cARHZvbEelG4BEdsEsRocwAER3I2BIh0ugRHdfmkbuQABEd5UCR4QmgER3yAhG1CAARHgOoEdS6wBEeF/USARiQER4tehIcE9ARHkKkkaBXgBEeYp4SAafgER5seZBuAAARHnjREbCJABEehN2SPVaYER6Ra5AQAAARHqqTkdp6ABEetu6QAAAAER7P/hHNpIARHuE+Ed3BgBEe+wWSJzRgER8PGBGnBQARHyAWkZv8ABEfNBSR0SfAER9GbBH3LeARH1eOEfpmwBEfbxkRkAAAER96bBHjr8ARH43XEg+RkBEfmViSBAaQER+oABH5kOARH7WOEgxUsBEfyIYR63mgER/TFBICDgARH9+OEj3vSBEf7lkSEa/AESAAuxHUn8ARIAjikaD+gBEgF1MR/fugESAoLxINCRARIDdtEcc4wBEgP4YR0VBAESBICRGTrwARIFJdEiV+WBEgWUQQgAAAESBkYhICjDARIG2qEaYqgBEgc2oRjm0AESCBRhHQPYARIIqDEhVgkBEgj5yQTAAAESCaLRIWlkARIKC2EBAAABEgtTSR4HYAESC80hGhRAARIMUWEhn0UBEgzxqSAyKwESDXzRHjccARIN+3EcQHQBEg5iIR2gAAESDtD5HDCgARIPZvkdPywBEg/9gR6DXgESEH9hHdssARIRGjkfD1ABEhGoUSChFwESEkBhIBpZARISl+EicEiBEhM28RpIMAESE5eJHUfQARIUSCke9QABEhUH0SH6xQESFWtxH8ucARIV3eD+AAABEhY0gRjaIAESFpjRHp8MARIW93D+AAABEhfgsR7ESgESGETZHzf2ARIY/5EZAGABEhnjERsCwAESGlYxIHTfARIa1NEaSPABEhs5QRxHAAESG5pZH4+iARIca6kfNgABEhzfoRu1SAESHX7ZHJGsARId1iEcFTABEh4ncR3hmAESHrVxH8hKARIfwGkdLYgBEiAUKRzTWAESIOWBHucwARIh+2EcEmgBEiJQAR1n5AESIw+JHgqAARIj8eEet3ABEiSb4SCnXAESJQ/ZGVdQARIllYEcOUQBEiYE2Rp9YAESJnqRGyNwARIm8uEeQPABEijTaR6eSAESKSvRGQeQARIpvqEfd7YBEioguRvMqAESKxCxHxnAARIrYLEBAAABEixN8SEIwQESLLxhIvcdARItR+EbFmgBEi200R0fLAESLhERA4AAARIueXEamlABEi8HIRzL8AESMB3BHT5IARIwdxEbk4ABEjESISWa2IESMYPhJCbcARIyHFEcrBwBEjKy8R4wigESNC0xGtC4ARI04BEdXOABEjZdyRdUwAESNtLRIDebARI3eqEf4FwBEjf84RzeAAESOEnhGkcIARI4zoEcTzQBEjlF0RwbGAESOdthH9HgARI67OEgDq4BEjukUR6rjAESPBThHupQARI8dxEeT3ABEj00oR6hMgESPc0pHCYsARI+SiEh5hsBEj72kSEI2gESP2ABBgAAARJAgLEe6q4BEkDaoRh8QAESQVP5HlCCARJBo5Ea24gBEkH88RygcAESQqJhHltaARJDBKEdSBABEkPJaSAQnQESRHcBILJ6ARJFMtEbUCgBEkWXQRnSQAESRk9hG87wARJG4NkgBB8BEkdj8R97rAESSCUBG7t4ARJIdzEWo6ABEkjaqRktQAESSXCZILCMARJJ9iEaPHgBEkqQ0SM36wESS4QhIApWARJMebkeSegBEk1AESLxdgESTZhJEzkAARJPKEEca+ABEk+UyRzsdAESUQpBHHPYARJRrJEcrXgBElI6oR+G4gESUpsxHb9UARJS93D+AAABElNiuRq5KAESU7VRAgAAARJUFKEar2ABElWugRxxvAESVhERIZsyARJW7XEc8YABElc9IRw7iAESWN4hGje4ARJZSFEg36IBElnl0RxbzAESWjxRG624ARJauREg5d4BEltMQRwn1AESW6QZH3naARJcU7Ec/+gBElzZ8R+OWAESXTaZAoAAARJd0BkkRkABEl+I6RyOvAESX9mRHObsARJgaFkXBmABEmE+kR8LDAESYZ9pHV9oARJh93EBAAABEmMEQSbmS4ESY5kBInWXARJj8REGAAABEmSbUR5/GAESZUvxHYVkARJlmsEcr7wBEmYFURfgoAESZufRHt0AARJnwREfvvYBEmhViR5vkgESaaThHSKgARJqFVECAAABEmqB4R5HuAESawVJHgUWARJsIBkW/WABEmy80R3JSAESbSLRGoDIARJt1gEiWZKBEm6BcR2tfAEScBLRHrUQARJxcSEgoIcBEnKAARuPWAEScz3RF6zAARJzuGEhFQMBEnTikSAhtwESdTmJHeXUARJ1tnEfToQBEnYVUQAAAAESdwJRIAAIARJ3UyEdY7gBEngIWRqC0AESeOhJHqluARJ5S/kbc9gBEnm5cRjCwAESemdBG/aAARJ7qpETuIABEn1AQRwsCAESfu9pHOR4ARJ/nCEbtsgBEoABUR4U+AESgGcRHc5YARKAvtEcrOQBEoGXASEQugESgsJZHHlUARKDbTkdKHQBEoPowRzDEAEShV9hFszAARKFvAEh2D8BEoY3QRp5+AESiHmJIZz2ARKIzND+AAABEokcERro6AESiY1hHc+cARKJ5skbPZgBEorZIRuc2AESjCkZEnCAARKMohEfSAoBEo3QeRhjUAESjn7xG3wwARKPpmkeGrIBEpHWwRoGuAESksjhGVMgARKTwzEZhFABEpR2eRrYuAESlQCxI+ICARKVgXEhxSIBEpXhURxChAESlutZHXZYARKYFzkg+kUBEpiiGRsVkAESmVtZGN9QARKZ99EfuhYBEppMyQEAAAESmzWZG6bYARKdVikgIU0BEp382R8HigESnmOJAQAAARKfayEiBKYBEqA8ARn2MAESoJMBH7HEARKg9BEex2YBEqFYkR4KgAESonkpG1pYARKi91EeXWwBEqQ0iR15IAESpODhIH9bARKlbZkar7gBEqYDeRqIAAESpqD5HQHIARKnaNkewKoBEqfmIR69EAESqPdhHMmYARKpRED+AAABEqnz+SKOkAESqqqZGj2oARKrSvkgMpQBEqxfWR2LeAESrW5pGn+IARKtx3EgbDoBEq6GWRw7aAESr3QRH5rOARKvztkiI0QBErA1SRvVkAESs1mBHXTgARK0GjkjmsuBErRsuR1+AAEStLthIgglARK1IiD+AAABErbBIR0k+AESt3ExFqtgARK4x8EcJdgBErklCR25/AESuXOBIiOygR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+ </scan>
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+
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+ <scan num="2"
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+ msLevel="2"
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+ peaksCount="56"
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+ polarity="+"
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+ scanType="full"
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+ centroided="1"
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+ retentionTime="PT1.900000S"
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+ startMz="95.0000"
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+ endMz="795.0000"
51
+ lowMz="111.9760"
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+ highMz="781.0853"
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+ basePeakMz="149.0495"
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+ basePeakIntensity="2852380.0000"
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+ totIonCurrent="9755125.0000">
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+ <precursorMz precursorIntensity="6986078.000000"
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+ collisionEnergy="35.000000">391.045410</precursorMz>
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+ <peaks precision="32">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</peaks>
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+ </scan>
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+
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+ <scan num="3"
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+ msLevel="2"
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+ peaksCount="51"
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+ polarity="+"
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+ scanType="full"
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+ centroided="1"
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+ retentionTime="PT2.750000S"
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+ startMz="110.0000"
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+ endMz="905.0000"
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+ lowMz="159.8986"
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+ highMz="482.0345"
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+ polarity="+"
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+ retentionTime="PT6.500000S"
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+ lowMz="112.1084"
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139
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140
+ centroided="1"
141
+ retentionTime="PT7.470000S"
142
+ startMz="325.0000"
143
+ endMz="2000.0000"
144
+ lowMz="442.1698"
145
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146
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159
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163
+ lowMz="387.0148"
164
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165
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+ startMz="300.0000"
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+ endMz="1500.0000"
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+ lowMz="300.6549"
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184
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245
+ </scan>
246
+
247
+ <scan num="13"
248
+ msLevel="1"
249
+ peaksCount="849"
250
+ polarity="+"
251
+ scanType="full"
252
+ centroided="1"
253
+ retentionTime="PT16.400000S"
254
+ startMz="300.0000"
255
+ endMz="1500.0000"
256
+ lowMz="300.4846"
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+ highMz="1494.3994"
258
+ basePeakMz="390.9473"
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+ basePeakIntensity="4595285.0000"
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+ centroided="1"
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+ retentionTime="PT17.770000S"
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+ startMz="110.0000"
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+ lowMz="149.2284"
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281
+ </scan>
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+ <scan num="15"
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+ msLevel="2"
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+ peaksCount="79"
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+ polarity="+"
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+ scanType="full"
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+ centroided="1"
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+ retentionTime="PT18.770000S"
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+ startMz="295.0000"
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+ endMz="2000.0000"
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