[BioPython] Problem with GenBank file

[Peter Bienstman]

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Hi Lee,

I've updated cvs to include the keywords 'Precursor' and 'derived_from'. If 
you update to a CVS version (and more specifically the file 
Bio/GenBank/genbank_format.py) you should be fine.

Cheers,

Peter

On Thursday 18 December 2003 17:00, Lee R. Shekter wrote:
> 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
>
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython

- -- 
- ------------------------------------------------
Peter Bienstman
Ghent University, Dep. of Information Technology
Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium
tel: +32 9 264 34 45, fax: +32 9 264 35 93
WWW: http://photonics.intec.UGent.be
email: Peter.Bienstman at UGent.be
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