[BioPython] problem with GenBank

[Iddo Friedberg]

Hi Maurice,

Try narrowing down your initial search space. For example:
GenBank.search_for('OCT4', database='protein')

or:

GenBank.search_for('OCT4', database='nucleotide')

This actualy completes, although slower.

I am puzzled by why this is so slow myself, expecially as other queries 
seem to complete in reasonable time. If anyone out there has any ideas, 
please share them with us.

./I

Maurice Ling wrote:

> Hi,
>
> I'm using BioPython 1.41 with Python 2.4.1. I'm trying to use GenBank 
> module,
>
> Python 2.4.1 (#1, Sep 16 2005, 17:46:53)
> [GCC 4.0.0 (Apple Computer, Inc. build 5026)] on darwin
> Type "help", "copyright", "credits" or "license" for more information.
> >>> from Bio import GenBank
> >>> GenBank.search_for('OCT4')
>
> But this takes forever. Any idea?
>
> Cheers
> Maurice
>
>
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-- 
Iddo Friedberg, Ph.D.
Burnham Institute for Medical Research
10901 N. Torrey Pines Rd.
La Jolla, CA 92037 USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9949
http://ffas.ljcrf.edu/~iddo