[BioPython] New User problem with GenBank

[Peter Bienstman]

FYI, I've confirmed that the parsing errors don't occur with the current CVS 
version, so the fix should be in the upcoming new release.

Cheers,

Peter

On Friday 04 July 2003 22:26, Cheung Auyeung wrote:
> Hi
>
> I try to follow the GenBank tortorila from the Biopython Tutorial and
> Cookbook and I get the following error messages:
>
> auyeung at sunday auyeung]$ python
> Python 2.2.2 (#1, Feb 24 2003, 19:13:11)
> [GCC 3.2.2 20030222 (Red Hat Linux 3.2.2-4)] on linux2
> Type "help", "copyright", "credits" or "license" for more information.
>
>  >>> from Bio import GenBank
>  >>> gi_list = GenBank.search_for("Opuntia AND rpl16")
>  >>> record_parser = GenBank.FeatureParser()
>  >>> ncbi_dict = GenBank.NCBIDictionary(parser = record_parser)
>  >>> gb_seqrecord = ncbi_dict[gi_list[0]]
>
> Traceback (most recent call last):
>    File "<stdin>", line 1, in ?
>    File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
> 1563, in __getitem__
>      return self.parser.parse(handle)
>    File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
> 268, in parse
>      self._scanner.feed(handle, self._consumer)
>    File "/usr/lib/python2.2/site-packages/Bio/GenBank/__init__.py", line
> 1255, in feed
>      self._parser.parseFile(handle)
>    File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 338,
> in parseFile
>      self.parseString(fileobj.read())
>    File "/usr/lib/python2.2/site-packages/Martel/Parser.py", line 366,
> in parseString
>      self._err_handler.fatalError(result)
>    File "/usr/lib/python2.2/site-packages/_xmlplus/sax/handler.py", line
> 38, in fatalError
>      raise exception
> Martel.Parser.ParserPositionException: error parsing at or beyond
> character 1108
>
> Any suggestion to fix the problem?
>
> Thanks
>
> Cheung
>
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> http://biopython.org/mailman/listinfo/biopython

-- 
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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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