Hi Datta, I made a python module to parse mzxml file, especially for peak list. It may be helpful for your work. http://code.google.com/p/massspec-toolbox/source/browse/#svn/trunk/mzxml
Here is the example code to use this module to parse MS1 intensities. http://code.google.com/p/massspec-toolbox/source/browse/trunk/mzxml/mzxml2ms1.py Just for decoding function (in MzXML.py): ---- def decode_spectrum(self,line): decoded = base64.decodestring(line) tmp_size = len(decoded)/4 unpack_format1 = ">%dL" % tmp_size idx = 0 mz_list = [] intensity_list = [] for tmp in struct.unpack(unpack_format1,decoded): tmp_i = struct.pack("I",tmp) tmp_f = struct.unpack("f",tmp_i)[0] if( idx % 2 == 0 ): mz_list.append( float(tmp_f) ) else: intensity_list.append( float(tmp_f) ) idx += 1 ---- Hope to be helpful. Taejoon On Jan 22, 11:00 am, datta <[email protected]> wrote: > If there is someone who could help: I have been trying to extract > peaklists frm mzXML in Python. I outlined below what i am trying to > do. Clearly, I don't understand something, but can't quite figure out > what I am missing. > > Rgds, > Datta. > > 1) I am trying to extract peak-lists from mzXML in Python. The > original section of mzXML is as follows: > > <scan num="1" > msLevel="1" > peaksCount="270" > polarity="+" > scanType="Full" > filterLine="FTMS + p NSI Full ms [300.00-1600.00]" > retentionTime="PT300.123S" > lowMz="301.126" > highMz="1585.59" > basePeakMz="445.111" > basePeakIntensity="135443" > totIonCurrent="731403" > > <peaks precision="32" > byteOrder="network" > pairOrder="m/z-int" >Q5aQG0R3K/hDlpE6RVIn/ > 0OW12JED0lzQ5cRrkSObAdDlxJYRAD3mUOYHvJFjM65Q5h9ckP9BiRDmJ5vRAWJNUOad1lEAZ/ > zQ5qZO0UwRjpDnJCDRFeg5kOckZBGTL > +iQ5ym70Q24qVDnRHsRIfZK0OdW81EEGlxQ52SsEQKmUhDnZaERCM8pkOdn4pFFBTVQ56MykRRt > 11DnqOvRA1Hn0Ohq > +dEEbP8Q6M3H0P1a0FDo4AuRQzUwEOjiVlD6Af/Q6R/TUQaQYpDpH > +8RC9rs0OkkUhD6htlQ6Yi4kVmDXBDplc0RAk09UOnDO9EKudJQ6ePSkTx3JJDqD3jRBxMREOp7 > ndEICmbQ67tVEQRNQtDrxCKRDOYqkOvl2lD8S > +1Q7GHkkUHJqdDsgg/ > RDNPEEOyhvlEHCE0Q7KH7kQ2cyhDsxjpRBjaCEOzmTBEFLFPQ7b9m0QG11dDt6geRCMwj0O5icB > EqPh1Q7mKQkSdO29DuYwNR7j5e0O5p1ZExr2GQ7oEfkQr6cJDugqyREbEjkO6C > 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rtEdxxgRBc5lER4z2VEHJE0RHx3aEQrvN5EfJjlRBPZ50SBYCREM302RIF0hEQaQd5EgZETRCaB > AUSDgK9EIPZ2RIPGTUQiO4VEg9xBRCCWy0SEmYpEIv/ > dRIa3EEQd48VEh3mXRCL4GkSKi0xEeVHCRIqMOURNj1JEjJd9RBmPFkSNs9FEDtULRI3rD0Q1EM > hElB > +bRDaiFUScBBpEK2ozRJyp > +URVoDZEnTXXRBaChESdqXVEPYuXRJ3veERbiFVEnk1SRCsuLESeZ2dEJ5+ > +RJ53ZkQGzaJEopi6RNqrk0SimelEnqz+RKPqCUQZlN9EpeczRDcfWkSnVnREH1h/ > RKeOg0Qcs2lEqH2lRBx5JESrBbhEFpe5RK3XBkQMUlNErrpnRB5XgESx6O5ELsnnRLQwUUQZ/ > ONEuQ+HRB6RfES/ > LS1EQEpbRL9fZkQa6v1EwYDYRLR1i0TBgo9EP1V2RMGSVUQWcstEwZcIRFrTkETBo6tESMiwRML > SAUQUyL9Ew1LsRC2+xUTGMwFENI/ > 2</peaks> > </scan> > > 2) My python code > > >>> import base64 > >>> encoded = > >>> r'Q5aQG0R3K/hDlpE6RVIn/0OW12JED0lzQ5cRrkSObAdDlxJYRAD3mUOYHvJFjM65Q5h9ckP9B > >>> > >>> iRDmJ5vRAWJNUOad1lEAZ/zQ5qZO0UwRjpDnJCDRFeg5kOckZBGTL+iQ5ym70Q24qVDnRHsRIfZ > >>> > >>> K0OdW81EEGlxQ52SsEQKmUhDnZaERCM8pkOdn4pFFBTVQ56MykRRt11DnqOvRA1Hn0Ohq+dEEbP > >>> > >>> 8Q6M3H0P1a0FDo4AuRQzUwEOjiVlD6Af/Q6R/TUQaQYpDpH+8RC9rs0OkkUhD6htlQ6Yi4kVmDX > >>> > 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\xf6vD\x83\xc6MD";\x85D > \x83\xdcAD \x96\xcbD\x84\x99\x8aD"\xff\xddD\x86\xb7\x10D\x1d\xe3\xc5D > \x87y\x97D"\xf8\x1aD\x8a\x8bLDyQ\xc2D\x8a\x8c9DM\x8fRD\x8c\x97}D > \x19\x8f\x16D\x8d\xb3\xd1D\x0e\xd5\x0bD\x8d\xeb\x0fD5\x10\xc8D\x94\x1f > \x9bD6\xa2\x15D\x9c\x04\x1aD+j3D\x9c\xa9\xf9DU\xa06D\x9d5\xd7D > \x16\x82\x84D\x9d\xa9uD=\x8b\x97D\x9d\xefxD[\x88UD\x9eMRD+.,D\x9eggD > \'\x9f\xbeD\x9ewfD\x06\xcd\xa2D\xa2\x98\xbaD\xda\xab\x93D\xa2\x99\xe9D > \x9e\xac\xfeD\xa3\xea\tD\x19\x94\xdfD\xa5\xe73D7\x1fZD\xa7VtD\x1fX\x7fD > \xa7\x8e\x83D\x1c\xb3iD\xa8}\xa5D\x1cy$D\xab\x05\xb8D\x16\x97\xb9D\xad > \xd7\x06D\x0cRSD\xae\xbagD\x1eW\x80D\xb1\xe8\xeeD.\xc9\xe7D\xb40QD > \x19\xfc\xe3D\xb9\x0f\x87D\x1e\x91|d\xbf...@j[d\xbf_fd\x1a\xea\xfdd > \xc1\x80\xd8D\xb4u\x8bD\xc1\x82\x8fD?UvD\xc1\x92UD\x16r\xcbD > \xc1\x97\x08DZ\xd3\x90D\xc1\xa3\xabDH\xc8\xb0D\xc2\xd2\x01D > \x14\xc8\xbfD\xc3R\xecD-\xbe\xc5D\xc63\x01D4\x8f\xf6' > > Jimmy Eng said (in an earlier post) that we have to convert this to > little-endian and then start reading. This is where I am stuck. > Some of the things I tried: > > >>> from struct import * > >>> unpack('!>',data ) > > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > struct.error: bad char in struct format>>> unpack('!>L',data ) > > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > struct.error: bad char in struct format>>> unpack('!L',data ) > > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > struct.error: unpack requires a string argument of length 4 > > Here is the pyDoc link for struct package in > Python:http://docs.python.org/library/struct.html > > Thanks in advance. > > Regards, > Datta > Grad Student, Bioinformatics, UMICH. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. 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