[BioPython] Fwd: Biopython - SwissProt

[Jeffrey Chang]

---------- Forwarded message ----------
From: Jeffrey Chang <jeffrey.chang at duke.edu>
Date: Jan 6, 2007 12:08 PM
Subject: Re: Biopython - SwissProt
To: Kristian Rother <krother at genesilico.pl>
Cc: biopython at biopython.org


Hi Kristian,

Thank you very much for the fixes.  Looking through the mailing list,
it appears that there have been changes to the 1.42 and after the 1.42
version to handle updates to the Swiss-Prot format.  I do not know
whether these updates fix the same issues you have addressed.

I am forwarding your email and code to the biopython mailing list in
case someone else has more to add, or can integrate your changes.

Thanks,
Jeff


On 1/3/07, Kristian Rother <krother at genesilico.pl> wrote:
> Hi Jeffrey,
>
> The Swiss-Prot parser on my Biopython installation (1.41, Debian) failed
> to digest the whole uniprot/swissprot file. Made some improvements to
> the code. Now, it runs on all 250,000 entries of the current release.
> I recognized there is a 1.42 out already, but maybe the code is useful
> for someone else, anyway. If not, we needed this one now and we're happy
> with it.
>
> Details:
> Chimped my way through the current UniProt documentation. Tried not to
> break downward compatibility (but did not test it explicitly). Changed
> the parsing of the following records:
>  ID: made to conform the current standard.
>  OH: this is brand new.
>  RX: seemed outdated. In particular, a whitespace in SwissProt entry
> 62xxx caused me headaches.
>
> source is attached.
>
> best regards,
>
>    Kristian Rother
>
>    IIMCB Warsaw, Poland
>
>    http://www.rubor.de
>    http://www.genesilico.pl
>
>
>
>
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