[Biopython-dev] Biopython SwissProt bugs

Jeffrey Chang jchang at SMI.Stanford.EDU
Mon Mar 12 01:12:47 EST 2001

Thanks!  I've applied this patch against the current CVS.  Please test
this and close the bug if it works.

Also, it would be nice to have a sample entry for the regression testing


On Sun, 11 Mar 2001, Brad Chapman wrote:

> Hi OEyvind;
> (My sincerest apologies if I'm mangling your first name)
> Thanks for the bug reports for SwissProt (bugs 23 and 24 for those on
> the dev list). I fixed both of the problems, and have attached patches
> against the latest CVS version (which should also work with the latest
> release 1.00a1). I'm not positive if they will apply cleanly to
> 0.90d04, but that might be a good excuse for you to upgrade to the
> most recent release :-).
> For the RX line problem, it looks to me like SwissProt now uses RX
> lines like:
> RX   PubMed=9603189;
> in some places, where I guess they used to be:
> RX   MEDLINE; 85132727.
> This confused the parser, so I fixed it to check for and handle these
> new cases.
> For the second problem with the extra spaces in VARSPLIC lines, I just
> added a special case to check for this and correct it.
> These seem to work for me on the examples you provided -- if you could
> confirm that they work for you, that would be super.
> I'm sending the patch to the dev list so Jeff, the master o' SwissProt,
> can look it over before I check the changes and added tests into CVS.
> Thanks again for the bug reports.
> Brad

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