Read in the fragmentation_rules file.
#!/usr/bin/python ############################################################################## # file: config_fragrules.py # # 'msparser' toolkit example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2010 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Source: parser/examples/test_python/config_fragrules.py $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## import msparser import sys if len(sys.argv) < 2 : print(""" The location of 'fragmentation_rules' file has to be specified as a parameter. The location should either be the full path to the 'fragmentation_rules' file or a URL to a Mascot server - e.g. http://mascot-server/mascot/cgi """) sys.exit(1) # A sessionID can optionally be passed as the second parameter. # This will only be required if the 'file' is a URL. if len(sys.argv) > 2 : cs = msparser.ms_connection_settings() cs.setSessionID(sys.argv[2]) file = msparser.ms_fragrulesfile(sys.argv[1], cs) else : file = msparser.ms_fragrulesfile(sys.argv[1]) if not file.isValid() : print("There are errors. Cannot continue. The last error description:") print(file.getLastErrorString()) sys.exit(1) n = file.getNumberOfInstruments() print("%d instruments are configured:" % n) for i in range(n) : print(file.getInstrumentName(i)) # Now change ESI-QUAD-TOF. instrument = file.getInstrumentByName("ESI-QUAD-TOF") instrument.setSeriesUsed(23, 1) # Add v series file.updateInstrumentByName("ESY-QUAD-TOF", instrument) # And delete MALDI-QIT-TOF. file.deleteInstrumentByName("MALDI-QIT-TOF") # Finally, save the file under a new name. file.setFileName(sys.argv[1] + ".new"); file.save_file(); if not file.isValid() : print("Failed to save: %s" % file.getLastErrorString()) else : print("%s.new now has %d instruments configured" % (sys.argv[1], file.getNumberOfInstruments())) firstSeries = msparser.ms_fragmentationrules.getFirstSeries() firstSeries = msparser.ms_fragmentationrules.getFirstSeries() lastSeries = msparser.ms_fragmentationrules.getLastSeries() print("First series: %s" % firstSeries) print("Last series : %s" % lastSeries) for i in range(firstSeries, 1 + lastSeries) : print("--------- %d ---------" % i) print(msparser.ms_fragmentationrules.getSeriesName(i)) print(msparser.ms_fragmentationrules.getSeriesDescription(i)) """ Running the program as python config_fragfules.py /usr/local/mascot/config/fragmentation_rules will give the following output under Mascot Server 2.3: 14 instruments are configured: Default ESI-QUAD-TOF MALDI-TOF-PSD ESI-TRAP ESI-QUAD ESI-FTICR MALDI-TOF-TOF ESI-4SECTOR FTMS-ECD ETD-TRAP MALDI-QUAD-TOF MALDI-QIT-TOF MALDI-ISD CID+ETD /usr/local/mascot/config/fragmentation_rules.new now has 13 instruments configured First series: 4 Last series : 25 --------- 4 --------- immonium immonium --------- 5 --------- a a series --------- 6 --------- a* a - NH3 if a significant and fragment includes RKNQ --------- 7 --------- a0 a - H2O if a significant and fragment includes STED --------- 8 --------- b b series --------- 9 --------- b* b - NH3 if b significant and fragment includes RKNQ --------- 10 --------- b0 b - H2O if b significant and fragment includes STED --------- 11 --------- c c series --------- 12 --------- x x series --------- 13 --------- y y series --------- 14 --------- y* y - NH3 if y significant and fragment includes RKNQ --------- 15 --------- y0 y - H2O if y significant and fragment includes STED --------- 16 --------- z z series --------- 17 --------- yb internal yb < 700 Da --------- 18 --------- ya internal ya < 700 Da --------- 19 --------- y must be significant y or y++ must be significant --------- 20 --------- y must be highest score y or y++ must be highest scoring series --------- 21 --------- z+1 z+1 series --------- 22 --------- d d and d' series --------- 23 --------- v v series --------- 24 --------- w w and w' series --------- 25 --------- z+2 z+2 series """
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