[BioPython] Connecting to Genbank

[Glen Spraggon]

Hi Again,
          Thanks, I have found a work around for it to get the
information I need but it does seem that the GenBank.search_for function
is not working for gi numbers - it does work for text searches in the
script however.

Cheers

Glen


-----Original Message-----
From: Peter Bienstman [mailto:Peter.Bienstman at UGent.be] 
Sent: Wednesday, November 26, 2003 8:07 AM
To: Glen Spraggon; biopython at biopython.org
Subject: Re: [BioPython] Connecting to Genbank


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Ah, so it's not a parsing problem then.

I'm not familiar with the network access code to GenBank, so perhaps
somebody 
else can help you here.  Brad?

Peter

On Wednesday 26 November 2003 16:39, Glen Spraggon wrote:
> Hi Again,
>          No gi number that I have tried works there appears to be no 
> connection you can try gi|15834378 but the same sort of call works 
> with BioPerl.
>
> Cheers
>
> Glen
>
> -----Original Message-----
> From: Peter Bienstman [mailto:Peter.Bienstman at UGent.be]
> Sent: Tuesday, November 25, 2003 11:24 PM
> To: Glen Spraggon; biopython at biopython.org
> Subject: Re: [BioPython] Connecting to Genbank
>
> On Wednesday 26 November 2003 02:08, Glen Spraggon wrote:
> > Hi,
> >       I have just resurrected an old script ( about six months old) 
> > that queries Genbank for sequence information using the gi number. 
> > The
> >
> > scrips gets the gi information by calling
> >
> > Gi_list=Genbank.search_for("gi|number")
> >
> > Then sequence information is extracted from Gi_list. The problem is 
> > that although this used to work it now it doesn't. It doesn't throw 
> > an
> >
> > exception either just keeps going. Has something changed with 
> > Genbank.
>
> Could you send us the accession number where the problem occurs? 
> Otherwise it's hard to track down what happens ;-)
>
> Cheers,
>
> Peter

- -- 
- ------------------------------------------------
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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