[BioPython] New User problem with GenBank

[Peter Bienstman]

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]]

Hi Cheung,

GenBank searches currently time out for me, so I cannot reproduce the problem 
at the moment.

Have you tried upgrading to the latest CVS version of BioPython? It's possible 
that after the tutorial was written, additional new GenBank records now 
satisfy the search criterion, and that these new records need the fixes in 
CVS.

Hope this helps,

Peter

-- 
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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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