[BioPython] Uniprot Parser

[Peter]

On Mon, Feb 25, 2008 at 4:32 PM, Jonathan Boulais <biosql at hotmail.com> wrote:
>
>  Hi everyone,
>
>  I'm a little bit concerned about the speed of the parsing/loading of the Uniprot .dat files
>  into the Biosql database. It takes a hell of a time...

What version of Biopython are you using?

One thing you could try is timing a simple script that only reads in
the SwissProt file but doesn't do anything with the BioSQL database -
to try and get a feel for which bit is slow.

If its the parsing that is slow, you could try commenting out the bit
which deals with the EBI ** lines (see bug 2353 for details), namely
line 359 in CVS, self._skip_starstar(uhandle), and see if that makes a
big difference.

Peter