Hey everybody:
I am trying to convert my inspect output to pep.xml for downstream
analysis in the TPP (as documented:
http://tools.proteomecenter.org/wiki/index.php?title=Expert_search_and_TPP_usage).
Unfortunately I can't get this far as I am getting a series of errors
when trying to run the conversion script inspecttopepxml.py provided
with the inspect installation. I am running Windows 7 and have tried
both Python 2.5 and 2.7. My original .mzxml files are from Thermo
(Orbi) and Bruker (Q-FTICR) instruments respectively and appear
valid / will run in many all other programs tested.
The inspect search will run from these files and produce valid
results, however it stalls on the conversion with this messages
(following). Any help would be greatly appreciated!
Thanks,
-Chris
BRUKER results:
c:\Inspect\BrukerOrbi>c:\python\python.exe c:\inspect\brukerorbi
\inspecttopepxml
.py -i c:\inspect\brukerorbi\EtuSCX_B1_02.txt -o c:\inspect\brukerorbi
\ETSCX_B1_
02.pepxml -p c:\inspect\brukerorbi\inspect.params -m c:\inspect
\brukerorbi\
(psyco not found - running in non-optimized mode)
Traceback (most recent call last):
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 763, in
<module>
Fix.Main()
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 263, in Main
self.ConvertInspectToPepXML(self.InputFilePath)
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 388, in
ConvertInspectTo
PepXML
self.GetSpectrumInfoFromMzXML(SpectrumFilePath)
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 725, in
GetSpectrumInfoF
romMzXML
MzXMLparser.parse(File)
File "c:\python\lib\xml\sax\expatreader.py", line 107, in parse
xmlreader.IncrementalParser.parse(self, source)
File "c:\python\lib\xml\sax\xmlreader.py", line 123, in parse
self.feed(buffer)
File "c:\python\lib\xml\sax\expatreader.py", line 207, in feed
self._parser.Parse(data, isFinal)
File "c:\python\lib\xml\sax\expatreader.py", line 301, in
start_element
self._cont_handler.startElement(name, AttributesImpl(attrs))
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 694, in
startElement
attrs.get('retentionTime', None))
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 677, in
normalize_whites
pace
return ' '.join(text.split())
AttributeError: 'NoneType' object has no attribute 'split'
THERMO results:
c:\Inspect\BrukerOrbi>c:\python25\python.exe c:\inspect\brukerorbi
\inspecttopepx
ml.py -i c:\inspect\brukerorbi\ET_SCX_ORBI_01.txt -o c:\inspect
\brukerorbi\ET_SC
X_orbi_01.pepxml -p c:\inspect\brukerorbi\inspect.params -m c:\inspect
\brukerorb
i\
(psyco not found - running in non-optimized mode)
Traceback (most recent call last):
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 763, in
<module>
Fix.Main()
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 263, in Main
self.ConvertInspectToPepXML(self.InputFilePath)
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 388, in
ConvertInspectTo
PepXML
self.GetSpectrumInfoFromMzXML(SpectrumFilePath)
File "c:\inspect\brukerorbi\inspecttopepxml.py", line 725, in
GetSpectrumInfoF
romMzXML
MzXMLparser.parse(File)
File "c:\python25\lib\xml\sax\expatreader.py", line 107, in parse
xmlreader.IncrementalParser.parse(self, source)
File "c:\python25\lib\xml\sax\xmlreader.py", line 125, in parse
self.close()
File "c:\python25\lib\xml\sax\expatreader.py", line 217, in close
self.feed("", isFinal = 1)
File "c:\python25\lib\xml\sax\expatreader.py", line 211, in feed
self._err_handler.fatalError(exc)
File "c:\python25\lib\xml\sax\handler.py", line 38, in fatalError
raise exception
xml.sax._exceptions.SAXParseException: c:\inspect\brukerorbi
\ET_SCX_ORBI_01.mzXM
L:80828:416598: no element found
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