[Biopython-dev] New Biopython release coming up

Michiel de Hoon mdehoon at c2b2.columbia.edu
Mon Jul 3 01:21:00 UTC 2006

Peter wrote:
> Did anyone get back to you about the NBCI Blast XML format?  I would say 
> parsing blast output is a fairly important feature to a lot of users (I 
> may of course be biased)...
No response yet, but I'll ask them again before the upcoming release. 
The existing XML parser still works as advertised for single blast 
searches. For multiple blast searches, people will have to run a 
previous version of blast locally.

> Bugzilla Bug 1997 VARCHAR too small in SCOP tables
> http://bugzilla.open-bio.org/show_bug.cgi?id=1997
> Suggested fix looked OK to me, but as I've never used SCOP as second 
> opinion would be wise.

This one looks fine to me, but I'm not a SCOP user either.

> Bugzilla Bug 1987 Alphabet.Gapped does not retain gap character
> http://bugzilla.open-bio.org/show_bug.cgi?id=1987
> I have attached a suggested patch, second opinion welcome

Whereas the patch looks fine, I have no idea what this code is supposed 
to do, or why it needs to be so complicated.

> Bugzilla Bug 1946 Parsing GenBank Files - unknown line type PROJECT
> Does anyone use the new project line?  Would a simple string be enough 
> to store this?
 From NCBI's description, it appears they're not quite sure yet what 
this project line should look like (note that the project line in the 
description is different from the project line in the GenBank file: 
GenomeProject vs. GENOME_PROJECT). I would just store the line in a 
simple string, and do something more fancy once we know the proper format.

My 2¢.


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