[Biopython-dev] Uniprot parsers

[Peter]

On Thu, Nov 11, 2010 at 10:06 PM, Renato Alves
<rjalves at igc.gulbenkian.pt> wrote:
> Hi everyone,
>
> With the arrival of the Uniprot XML parser, is the swiss format still
> going to be maintained?

Definitely yes in the short term, for one thing the swiss files are
smaller and much faster to parse. I suspect UniProt themselves
may want to retire the swiss text format at some point, but moving
every user over to XML will take some time.

> I just clashed with a 'swiss' format parsing problem present in the
> 1.55b release (and previous releases). Seems like the format might have
> changed.
>
> One random case is [1] where all of the 2nd and following IDs are
> ignored by the parser. In Ensembl, for instance, the parser only
> collects the ENST (the 1st) but not the ENSP (2nd) and ENSG (3rd)
> identifiers.
>
> Is this a known issue?
>

No - could you file a bug one this with a short example to explain
what result you get, and what you want.

Thanks,

Peter