[Biopython-dev] Working on Sequence deprecation

[Brad Chapman]

Hi Jeff!

[Talking about Sequence.py deprecation]
> > I'd done a little bit of work on this earlier on Fasta.py, and I
> > completed the job this morning and checked it in along with tests.
> 
> Good.  Peter Wilkinson is working on a solution for parsing the
> description line better, with support for NCBI's formats.  This stuff
> should be coming in in the next few weeks or so.

Sweet! I'll be ready happy to see that -- it would be nice to have some 
robust functions for getting info from "standard" FASTA title lines.

[SProt.py patch]
> Great.  Please check your patch in.

Okee dokee. I also added a quick test for SProt.py, so that I
hopefully won't break anything in the future, and added a test case
that uses the 'OX' line.

> > Additionally, have we also thought about getting rid of the SeqIO
> > directory? I think the current Fasta.py will do everything this does
> > right now, so we might not need it any more. What do people think?
> 
> Let's leave the directory in for now, for future expansion.  Eventually,
> we should have a function (like bioperl's) where the user can point SeqIO
> to a sequence file, and it'll figure out how to parse it into a Seq class.

Cool, that makes good sense.

BTW, Jeff, I was going to nominate you on the main list to be the
biopython representative for BOSC 2001 -- do you want that
responsibility? I know you are just the man to do it, but I didn't
want to give you stuff to do you don't want! 

Brad