[BioPython] Problem with GenBank file

Lee R. Shekter lee at epigenomix.com
Thu Dec 18 11:00:00 EST 2003


I'm having a problem parsing a GenBank file. This problem has been
posted before and the solution has always been to run the latest version
of biopython, which I am doing (1.23). Do I need to get a newer version
from CVS? The error looks like this:

Traceback (most recent call last):
  File "../parsers/genbankparser.py", line 91, in ?
    GenBank2FASTA()
  File "../parsers/genbankparser.py", line 38, in GenBank2FASTA
    cur_record = feature_parser.parse(StringIO.StringIO(text_record))
  File "/usr/local/lib/python2.3/site-packages/Bio/GenBank/__init__.py",
line 229, in parse
    self._scanner.feed(handle, self._consumer)
  File "/usr/local/lib/python2.3/site-packages/Bio/GenBank/__init__.py",
line 1251, in feed
    self._parser.parseFile(handle)
  File "/usr/local/lib/python2.3/site-packages/Martel/Parser.py", line
328, in parseFile
    self.parseString(fileobj.read())
  File "/usr/local/lib/python2.3/site-packages/Martel/Parser.py", line
356, in parseString
    self._err_handler.fatalError(result)
  File "/usr/local/lib/python2.3/xml/sax/handler.py", line 38, in
fatalError
    raise exception
Martel.Parser.ParserPositionException: error parsing at or beyond
character 2141

The Accession # of the file in question is: NP_789740

Thanks, Lee Shekter



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