Maybe try this. http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList
I have used the matlab bio. toolbox and someone did put out a dist. platform that doesn't require the bio. toolbox and I will send along when I find it http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList Also for python mmass http://mmass.biographics.cz/ has some pretty good tools as does and http://blais.dfci.harvard.edu/index.php?id=63 script page http://blais.dfci.harvard.edu/index.php?id=96 On Mon, Jan 25, 2010 at 3:35 PM, Brian Pratt <[email protected]>wrote: > I wonder if anyone has done this for MatLab? (I know the bioinformatics > toolbox has mzXML read, but that's pretty spendy for some folks.) > > For that matter, I wonder what the entire list of languages would look > like? At this point I'm aware of C/C++, Java, and now Python. > - Brian > On Mon, Jan 25, 2010 at 12:24 PM, datta <[email protected]> wrote: > >> Taejoon, >> >> Thanks a lot! This is indeed very helpful. >> Thank you! >> >> Datta. >> >> On Jan 23, 11:23 am, Taejoon Kwon <[email protected]> >> wrote: >> > 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/m... >> > >> > 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 >> > > +xGCDvKQ7oNLERuBitDuiCoRArm5UO6i5VFsLhTQ7sL4ESCoJxDu4wDQ/ >> > > k38UPAjnlEEdg8Q8CSYkQngqxDwYDKRC1E6EPBghJEFRPIQ8IO/ >> > > >> 0R7iUpDwo07RJ7NPkPDodhEa7OdQ8OjZEarYUFDxCOwRTnj6UPHJnBD99gVQ8igCUQIpltDyNh6 >> Q/ >> > > WvhEPJFiZEVbLkQ818bkQp/rpDzqCVRJmoeUPRpxZFTr6zQ9In20SI6OZD06s+Q/ >> > > 59v0PWiaFEK/M+Q9ipnUQbVnFD2iqYRIJn10PboVFD/ >> > > >> G0zQ96Lg0TjBqdD3o45SAREokPekThEi4O+Q98OJ0bCyeBD343CRi9MXkPfj8VEayliQ9+r >> > > +UQQmx1D4A0ORI1kBkPgDe1EgteIQ+AoJ0QWENhD4I1SRISPa0PhDs1EDqGHQ >> > > +OpVEVQJ9pD5ZSaRN9wgEPnDm1ETrmMQ+cRiUeb0fJD55FoRkwj0UPnm55EDKY8Q >> > > +gOeEQhKvpD6BDZRa9GRkPokJpEFJXhQ+mLTkTCnc5D6gwGRGYH2kPqIidEDh1EQ >> > > +ojFkQFGoND7hfXRLAeOUP1FRFFTdvNQ/UdFkQlMZhD9ZSuRD/xGUP1t3pEJrAIQ/YU >> > > +USoDnND9vo6RCZ9+0P5jXVEDooyQ/rzNkQ5CJxD+vTKRCgsbEP695JENy3nQ/ >> > > r4p0RMsoVD/JMHRAaBiEQAe2NEFPpxRAG4SUQ2hcVEAcgxRwXKykQCB/ >> > > dFn8ZRRAIIz0RN8GlEAhAPRBVmZ0QCR+JFQt >> > > >> +QRAKHwURJXYFEBcukRFFC3EQGCCpEUakbRAYJ4UcDlBZEBkj1RJt8XUQGSatFgpc9RAaJSkTFp >> cpEBopJRCl8QUQGyWFETTiyRAmM8UT0Py9ECfUfRApsBEQNC7ZFH1D1RA1Lg0SHua1EEIfARC1e >> L0QR7pJEGtcbRBNUW0P0ubBEE7UNRBPLvUQUSThF06i2RBSJQUTSiNlEFMidRGQP2UQVCQZEMKc >> 8RBVJHUQMdfFEF4UnREgAy0QXjDpEbo1GRBeQckR5w7REF5I0RCK7ZUQXlLFEEgxLRBfMf0SYuX >> pEGAxoREr6C0QYit5FsgouRBjK40TgEslEGQrhRL5UnEQbI4BECxaVRBt7+EQJa4NEHA4rRIzTh >> 0QcNodEMpRBRBxOQUQySJ5EHTQFRBLSi0QehWNEGFcORB >> > > >> +M3ER1YEVEH8yiRFrOtEQgDQVEGUFURCE62UQHfatEIgjbRE0UdEQiCbREX5XzRCVoaEQOsGREJ >> spVROOUakQnCb9EaEmsRCdKIkQsA/ >> > > JEKfcBRCi1XUQqQI9EIHOlRCsLx0SQd >> > > +dEK0v9RIteTUQry0FEJINKRCxOv0QUP5hELfl5REWyGkQyThRD/ >> > > IoPRDbr80RoxRJEOAQURCqeukQ5S0JEPpwtRDnLSkRN3V1EPZg >> > > >> +RFXVhkRBRa9EFmcZREGR1kQUV5FEQmAyRB4vnkRDOKlENxxrREn320QiCwRETI3QRB4QxERMzg >> 9EDBw2REzQQ0Q1MilETNq >> > > +RETAMkRM44lENEIHREz6vkQOT3ZETxTTRDg+YERQH8dEnPPQRFAg3ERB4fpEVdLBRBe/ >> > > >> +ERW7+pEPywrRFdWfEQTt1REWekoRCIcpERd48lEMuvvRF4COkQNyjdEXtpPRBxQm0Rhe61EL7N >> LRGG3/ >> > > kQVPuZEYrePRDj/HkRkkNdEdTd6RGXzJkQEWB5EZwacRB7wG0RoQyhEC/ >> > > >> +XRGus9kQjkqhEa7nCRDkXqkRu6xVEsQtPRG8yjUQkSEtEc9wuRByVzUR0bldEIy6TRHXI9EQIK >> 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 >> BDplc0RAk09UOnDO9EKudJQ6ePSkTx3JJDqD3jRBxMREOp7ndEICmbQ67tVEQRNQtDrxCKRDOYq >> kOvl2lD8S+1Q7GHkkUHJqdDsgg/RDNPEEOyhvlEHCE0Q7KH7kQ2cyhDsxjpRBjaCEOzmTBEFLFP >> Q7b9m0QG11dDt6geRCMwj0O5icBEqPh1Q7mKQkSdO29DuYwNR7j5e0O5p1ZExr2GQ7oEfkQr6cJ >> DugqyREbEjkO6C+xGCDvKQ7oNLERuBitDuiCoRArm5UO6i5VFsLhTQ7sL4ESCoJxDu4wDQ/k38U >> PAjnlEEdg8Q8CSYkQngqxDwYDKRC1E6EPBghJEFRPIQ8IO/0R7iUpDwo07RJ7NPkPDodhEa7OdQ >> 8OjZEarYUFDxCOwRTnj6UPHJnBD99gVQ8igCUQIpltDyNh6Q/WvhEPJFiZEVbLkQ818bkQp/rpD >> zqCVRJmoeUPRpxZFTr6zQ9In20SI6OZD06s+Q/59v0PWiaFEK/M+Q9ipnUQbVnFD2iqYRIJn10P >> boVFD/G0zQ96Lg0TjBqdD3o45SAREokPekThEi4O+Q98OJ0bCyeBD343CRi9MXkPfj8VEayliQ9 >> +r+UQQmx1D4A0ORI1kBkPgDe1EgteIQ+AoJ0QWENhD4I1SRISPa0PhDs1EDqGHQ+OpVEVQJ9pD5 >> ZSaRN9wgEPnDm1ETrmMQ+cRiUeb0fJD55FoRkwj0UPnm55EDKY8Q+gOeEQhKvpD6BDZRa9GRkPo >> kJpEFJXhQ+mLTkTCnc5D6gwGRGYH2kPqIidEDh1EQ+ojFkQFGoND7hfXRLAeOUP1FRFFTdvNQ/U >> dFkQlMZhD9ZSuRD/xGUP1t3pEJrAIQ/YU+USoDnND9vo6RCZ9+0P5jXVEDooyQ/rzNkQ5CJxD+v >> TKRCgsbEP695JENy3nQ/r4p0RMsoVD/JMHRAaBiEQAe2NEFPpxRAG4SUQ2hcVEAcgxRwXKykQCB >> /dFn8ZRRAIIz0RN8GlEAhAPRBVmZ0QCR+JFQt+QRAKHwURJXYFEBcukRFFC3EQGCCpEUakbRAYJ >> 4UcDlBZEBkj1RJt8XUQGSatFgpc9RAaJSkTFpcpEBopJRCl8QUQGyWFETTiyRAmM8UT0Py9ECfU >> fRApsBEQNC7ZFH1D1RA1Lg0SHua1EEIfARC1eL0QR7pJEGtcbRBNUW0P0ubBEE7UNRBPLvUQUST >> hF06i2RBSJQUTSiNlEFMidRGQP2UQVCQZEMKc8RBVJHUQMdfFEF4UnREgAy0QXjDpEbo1GRBeQc >> kR5w7REF5I0RCK7ZUQXlLFEEgxLRBfMf0SYuXpEGAxoREr6C0QYit5FsgouRBjK40TgEslEGQrh >> RL5UnEQbI4BECxaVRBt7+EQJa4NEHA4rRIzTh0QcNodEMpRBRBxOQUQySJ5EHTQFRBLSi0QehWN >> EGFcORB+M3ER1YEVEH8yiRFrOtEQgDQVEGUFURCE62UQHfatEIgjbRE0UdEQiCbREX5XzRCVoaE >> QOsGREJspVROOUakQnCb9EaEmsRCdKIkQsA/JEKfcBRCi1XUQqQI9EIHOlRCsLx0SQd+dEK0v9R >> IteTUQry0FEJINKRCxOv0QUP5hELfl5REWyGkQyThRD/IoPRDbr80RoxRJEOAQURCqeukQ5S0JE >> PpwtRDnLSkRN3V1EPZg+RFXVhkRBRa9EFmcZREGR1kQUV5FEQmAyRB4vnkRDOKlENxxrREn320Q >> iCwRETI3QRB4QxERMzg9EDBw2REzQQ0Q1MilETNq'RETAMkRM44lENEIHREz6vkQOT3ZETxTTRD >> g+YERQH8dEnPPQRFAg3ERB4fpEVdLBRBe/+ERW7+pEPyw'RFdWfEQTt1REWekoRCIcpERd48lEM >> uvvRF4COkQNyjdEXtpPRBxQm0Rhe61EL7NLRGG3/kQVPuZEYre'RDj/HkRkkNdEdTd6RGXzJkQE >> WB5EZwacRB7wG0RoQyhEC/+XRGus9kQjkqhEa7nCRDkXqkRu6xVEsQt'RG8yjUQkSEtEc9wuRBy >> VzUR0bldEIy6TRHXI9EQIKrtEdxxgRBc5lER4z2VEHJE0RHx3aEQrvN5EfJj'RBPZ50SBYCREM3 >> 02RIF0hEQaQd5EgZETRCaBAUSDgK9EIPZ2RIPGTUQiO4VEg9xBRCCWy0SEmYpEIv/'RIa3EEQd4 >> 8VEh3mXRCL4GkSKi0xEeVHCRIqMOURNj1JEjJd9RBmPFkSNs9FEDtULRI3rD0Q1EMhElB+'RDai >> FUScBBpEK2ozRJyp+URVoDZEnTXXRBaChESdqXVEPYuXRJ3veERbiFVEnk1SRCsuLESeZ2dEJ5+ >> 'RJ53ZkQGzaJEopi6RNqrk0SimelEnqz+RKPqCUQZlN9EpeczRDcfWkSnVnREH1h/RKeOg0Qcs2 >> lEqH2'RBx5JESrBbhEFpe5RK3XBkQMUlNErrpnRB5XgESx6O5ELsnnRLQwUUQZ/ONEuQ+HRB6Rf >> ES/LS1EQEp'RL9fZkQa6v1EwYDYRLR1i0TBgo9EP1V2RMGSVUQWcstEwZcIRFrTkETBo6tESMiw >> RMLSAUQUyL9Ew1L'RC2+xUTGMwFENI/2' >> s >> > > >>> data = base64.b64decode(encoded) >> > > >>> data >> > >> > > 'C\x96\x90\x1bDw+\xf8C\x96\x91:ER\'\xffC\x96\xd7bD\x0fIsC\x97\x11\xaeD >> > > \x8el\x07C\x97\x12XD\x00\xf7\x99C\x98\x1e\xf2E\x8c\xce\xb9C\x98}rC\xfd >> > > \x06$C\x98\x9eoD\x05\x895C\x9awYD\x01\x9f\xf3C\x9a\x99;E0F:C\x9c >> > > \x90\x83DW\xa0\xe6C\x9c\x91\x90FL\xbf\xa2C\x9c\xa6\xefD6\xe2\xa5C\x9d >> > > \x11\xecD\x87\xd9+C\x9d[\xcdD\x10iqC\x9d\x92\xb0D\n\x99HC\x9d >> > > \x96\x84D#<\xa6C\x9d\x9f\x8aE\x14\x14\xd5C\x9e\x8c\xcaDQ\xb7]C\x9e >> > > \xa3\xafD\rG\x9fC\xa1\xab\xe7D\x11\xb3\xfcC\xa37\x1fC\xf5kAC\xa3\x80.E >> > > >> \x0c\xd4\xc0C\xa3\x89YC\xe8\x07\xffC\xa4\x7fMD\x1aA\x8aC\xa4\x7f\xbcD/k >> > > \xb3C\xa4\x91HC\xea\x1beC\xa6"\xe2Ef\rpC\xa6W4D\t4\xf5C\xa7\x0c\xefD* >> > > \xe7IC\xa7\x8fJD\xf1\xdc\x92C\xa8=\xe3D\x1cLDC\xa9\xeewD )\x9bC\xae >> > > \xedTD\x115\x0bC\xaf\x10\x8aD3\x98\xaaC\xaf\x97iC\xf1/\xb5C >> > > \xb1\x87\x92E\x07&\xa7C\xb2\x08?D3O\x10C\xb2\x86\xf9D\x1c!4C >> > > >> \xb2\x87\xeeD6s(C\xb3\x18\xe9D\x18\xda\x08C\xb3\x990D\x14\xb1OC\xb6\xfd >> > > \x9bD\x06\xd7WC\xb7\xa8\x1eD#0\x8fC\xb9\x89\xc0D\xa8\xf8uC\xb9\x8aBD >> > > >> \x9d;oC\xb9\x8c\rG\xb8\xf9{C\xb9\xa7VD\xc6\xbd\x86C\xba\x04~D+\xe9\xc2C >> > > \xba\n\xb2DF\xc4\x8eC\xba\x0b\xecF\x08;\xcaC\xba\r,Dn\x06+C\xba >> \xa8D\n >> > > >> \xe6\xe5C\xba\x8b\x95E\xb0\xb8SC\xbb\x0b\xe0D\x82\xa0\x9cC\xbb\x8c\x03C >> > > >> \xf97\xf1C\xc0\x8eyD\x11\xd8<C\xc0\x92bD\'\x82\xacC\xc1\x80\xcaD-D\xe8C >> > > \xc1\x82\x12D\x15\x13\xc8C\xc2\x0e\xffD{\x89JC\xc2\x8d;D\x9e\xcd>C >> > > \xc3\xa1\xd8Dk\xb3\x9dC\xc3\xa3dF\xabaAC\xc4#\xb0E9\xe3\xe9C\xc7&pC >> > > \xf7\xd8\x15C\xc8\xa0\tD\x08\xa6[C\xc8\xd8zC\xf5\xaf\x84C\xc9\x16&DU >> > > \xb2\xe4C\xcd|nD)\xfe\xbaC\xce\xa0\x95D\x99\xa8yC\xd1\xa7\x16EN\xbe >> > > \xb3C\xd2\'\xdbD\x88\xe8\xe6C\xd3\xab>C\xfe}\xbfC\xd6\x89\xa1D+\xf3>C >> > > \xd8\xa9\x9dD\x1bVqC\xda*\x98D\x82g\xd7C\xdb\xa1QC\xfcm3C\xde\x8b\x83D >> > > \xe3\x06\xa7C\xde\x8e9H\x04D\xa2C\xde\x918D\x8b\x83\xbeC\xdf\x0e\'F >> > > \xc2\xc9\xe0C\xdf\x8d\xc2F/L^C\xdf\x8f\xc5Dk)bC\xdf\xab\xf9D\x10\x9b >> > > >> \x1dC\xe0\r\x0eD\x8dd\x06C\xe0\r\xedD\x82\xd7\x88C\xe0(\'D\x16\x10\xd8C >> > > \xe0\x8dRD\x84\x8fkC\xe1\x0e\xcdD\x0e\xa1\x87C\xe3\xa9TEP\'\xdaC >> > >> > ... >> > >> > read more ยป >> >> -- >> 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]<spctools-discuss%[email protected]> >> . >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post 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