[BioPython] SProt module

[Peter (BioPython List)]

Chris Fields wrote:
>> Hi all,
>>
>> SProt module no longer seems to work with current version of 
>> Uniprot KB  database. do anyone have work around for this module ? 
>>
>> regards,
>> KM
> 
> There have been recent changes in the format for the ID line in
> UniProt/SwisProt files, which could be part of the problem.  We just fixed
> this in BioPerl; not sure how it would be handled in BioPython.

Hi KM

As Chris points out, there have been a few format changes.  I'm pretty
sure that BioPython has been updated to cope:

Bug 2131 - SProt.py fails to parse the current Swiss-Prot version 51.0
http://bugzilla.open-bio.org/show_bug.cgi?id=2131
Fixed

Bug 2043 - SProt.py fails to parse the current Swiss-Prot version (RX
and OH lines are broken)
http://bugzilla.open-bio.org/show_bug.cgi?id=2043
Fixed

These changes where made after BioPython 1.42 was released.

I'm pretty sure that all you need to do is update the file
Bio/SwissProt/SProt.py in your python site-library with the version from
CVS, available here:

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SwissProt/SProt.py?cvsroot=biopython

(Or, if you would rather, get the entire latest source code from CVS,
and build and install that).

If you find a problem with that code, then please let us know (ideally
by logging a new bug).

Peter