[BioPython] Martel Parser error...
Michael Mayhew
mmayhew at mcb.mcgill.ca
Tue Jul 10 18:08:18 UTC 2007
Greetings,
I am using BioPython-1.42 (also tried 1.43) on Mac OS X (10.4.8) and
have successfully compiled/installed the prerequisite packages (Numeric
and mxTextTools).
I have been receiving a Martel Parser error as detailed in the
following readout (from a python interactive session), when I try to use
either Fasta.RecordParser() or Fasta.SequenceParser() instances:
>>tester = iter.next()
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Bio/Fasta/__init__.py",
line 72, in next
result = self._iterator.next()
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Martel/IterParser.py",
line 152, in iterateFile
self.header_parser.parseString(rec)
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/Martel/Parser.py",
line 356, in parseString
self._err_handler.fatalError(result)
File
"/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/xml/sax/handler.py",
line 38, in fatalError
raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond
character 0
I confirmed this when I ran the included test suites (with python
setup.py test).
I have seen some suggestions to get the most recent CVS version of
biopython to rectify this problem. How would I go about this?
Is getting the most recent CVS version of biopython the only/best
thing to do?
Thanks in advance.
Michael Mayhew
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