Extracting peak-lists from mzXML in "Python"
datta
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
+iQ5ym70Q24qVDnRHsRIfZK0OdW81EEGlxQ52SsEQKmUhDnZaERCM8pkOdn4pFFBTVQ56MykRRt11DnqOvRA1Hn0Ohq
+dEEbP8Q6M3H0P1a0FDo4AuRQzUwEOjiVlD6Af/Q6R/TUQaQYpDpH
+8RC9rs0OkkUhD6htlQ6Yi4kVmDXBDplc0RAk09UOnDO9EKudJQ6ePSkTx3JJDqD3jRBxMREOp7ndEICmbQ67tVEQRNQtDrxCKRDOYqkOvl2lD8S
+1Q7GHkkUHJqdDsgg/
RDNPEEOyhvlEHCE0Q7KH7kQ2cyhDsxjpRBjaCEOzmTBEFLFPQ7b9m0QG11dDt6geRCMwj0O5icBEqPh1Q7mKQkSdO29DuYwNR7j5e0O5p1ZExr2GQ7oEfkQr6cJDugqyREbEjkO6C
+xGCDvKQ7oNLERuBitDuiCoRArm5UO6i5VFsLhTQ7sL4ESCoJxDu4wDQ/
k38UPAjnlEEdg8Q8CSYkQngqxDwYDKRC1E6EPBghJEFRPIQ8IO/
0R7iUpDwo07RJ7NPkPDodhEa7OdQ8OjZEarYUFDxCOwRTnj6UPHJnBD99gVQ8igCUQIpltDyNh6Q/
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59v0PWiaFEK/M+Q9ipnUQbVnFD2iqYRIJn10PboVFD/
G0zQ96Lg0TjBqdD3o45SAREokPekThEi4O+Q98OJ0bCyeBD343CRi9MXkPfj8VEayliQ9+r
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r4p0RMsoVD/JMHRAaBiEQAe2NEFPpxRAG4SUQ2hcVEAcgxRwXKykQCB/
dFn8ZRRAIIz0RN8GlEAhAPRBVmZ0QCR+JFQt
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JEKfcBRCi1XUQqQI9EIHOlRCsLx0SQd
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IoPRDbr80RoxRJEOAQURCqeukQ5S0JEPpwtRDnLSkRN3V1EPZg
+RFXVhkRBRa9EFmcZREGR1kQUV5FEQmAyRB4vnkRDOKlENxxrREn320QiCwRETI3QRB4QxERMzg9EDBw2REzQQ0Q1MilETNq
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kQVPuZEYrePRDj/HkRkkNdEdTd6RGXzJkQEWB5EZwacRB7wG0RoQyhEC/
+XRGus9kQjkqhEa7nCRDkXqkRu6xVEsQtPRG8yjUQkSEtEc9wuRByVzUR0bldEIy6TRHXI9EQIKrtEdxxgRBc5lER4z2VEHJE0RHx3aEQrvN5EfJjlRBPZ50SBYCREM302RIF0hEQaQd5EgZETRCaBAUSDgK9EIPZ2RIPGTUQiO4VEg9xBRCCWy0SEmYpEIv/
dRIa3EEQd48VEh3mXRCL4GkSKi0xEeVHCRIqMOURNj1JEjJd9RBmPFkSNs9FEDtULRI3rD0Q1EMhElB
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RKeOg0Qcs2lEqH2lRBx5JESrBbhEFpe5RK3XBkQMUlNErrpnRB5XgESx6O5ELsnnRLQwUUQZ/
ONEuQ+HRB6RfES/
LS1EQEpbRL9fZkQa6v1EwYDYRLR1i0TBgo9EP1V2RMGSVUQWcstEwZcIRFrTkETBo6tESMiwRMLSAUQUyL9Ew1LsRC2+xUTGMwFENI/
2</peaks>
</scan>
2) My python code
>>> import base64
>>> encoded = r'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'RETAMkRM44lENEIHREz6vkQOT3ZETxTTRDg+YERQH8dEnPPQRFAg3ERB4fpEVdLBRBe/+ERW7+pEPyw'RFdWfEQTt1REWekoRCIcpERd48lEMuvvRF4COkQNyjdEXtpPRBxQm0Rhe61EL7NLRGG3/kQVPuZEYre'RDj/HkRkkNdEdTd6RGXzJkQEWB5EZwacRB7wG0RoQyhEC/+XRGus9kQjkqhEa7nCRDkXqkRu6xVEsQt'RG8yjUQkSEtEc9wuRByVzUR0bldEIy6TRHXI9EQIKrtEdxxgRBc5lER4z2VEHJE0RHx3aEQrvN5EfJj'RBPZ50SBYCREM302RIF0hEQaQd5EgZETRCaBAUSDgK9EIPZ2RIPGTUQiO4VEg9xBRCCWy0SEmYpEIv/'RIa3EEQd48VEh3mXRCL4GkSKi0xEeVHCRIqMOURNj1JEjJd9RBmPFkSNs9FEDtULRI3rD0Q1EMhElB+'RDaiFUScBBpEK2ozRJyp+URVoDZEnTXXRBaChESdqXVEPYuXRJ3veERbiFVEnk1SRCsuLESeZ2dEJ5+'RJ53ZkQGzaJEopi6RNqrk0SimelEnqz+RKPqCUQZlN9EpeczRDcfWkSnVnREH1h/RKeOg0Qcs2lEqH2'RBx5JESrBbhEFpe5RK3XBkQMUlNErrpnRB5XgESx6O5ELsnnRLQwUUQZ/ONEuQ+HRB6RfES/LS1EQEp'RL9fZkQa6v1EwYDYRLR1i0TBgo9EP1V2RMGSVUQWcstEwZcIRFrTkETBo6tESMiwRMLSAUQUyL9Ew1L'RC2+xUTGMwFENI/2' s
>>> data = base64.b64decode(encoded)
>>> data
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\x06\x9cD\x1e\xf0\x1bDhC(D\x0b\xff\x97Dk\xac\xf6D#\x92\xa8Dk
\xb9\xc2D9\x17\xaaDn\xeb\x15D\xb1\x0bODo2\x8dD$HKDs\xdc.D\x1c
\x95\xcdDtnWD#.\x93Du\xc8\xf4D\x08*\xbbDw\x1c`D\x179\x94Dx\xcfeD\x1c
\x914D|whD+\xbc\xdeD|\x98\xe5D\x13\xd9\xe7D\x81`$D3}6D\x81t\x84D\x1aA
\xdeD\x81\x91\x13D&\x81\x01D\x83\x80\xafD \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--D@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.
Taejoon Kwon
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
> >>> 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
datta
Thanks a lot! This is indeed very helpful.
Thank you!
Datta.
On Jan 23, 11:23 am, Taejoon Kwon <linusben.ute...@googlemail.com>
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...
> ...
>
> read more »
Brian Pratt
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Darryl Davis
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
Moshe Olshansky
Regards,
Moshe.
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Moshe Olshansky
Metabolomics Australia
Bio21 Molecular Science and Biotechnology Institute
The University of Melbourne
30 Flemington Road, Parkville, VIC 3010
Australia
voice: +61 3 8344 2201
e-mail: mos...@unimelb.edu.au
