[BioPython] Clustalw multiple alignment

[Brad Chapman]

Jeff wrote:
>  Since nobody objects, and a few people have expressed interest, let's
>  go ahead and plan to put this in.	

Will do. I will write up some tests and docs, and get it in there. Right
now it would be under Bio.Align -> does this sound good to people, or are
there other suggestions? I was just thinking that code generally dealing
with alignment stuff could go under here (as I mentioned, I would like to
do some pairwise alignment code as well).

>  Before you do, though, could you run a
>  quick check to see whether the existing code works under 1.6/2.0?  I'm
>  not sure if anyone's done this yet.	

I've been using it with 2.0b1 for a while now, without any problems
(although Andrew's reverse() function did pick up a bug in the beta
version!). So in general, I think the code is pretty happy with 2.0.

>  You could at a minimum run the
>  regression test suite, and pray it's comprehensive enough to catch 
>  problems!  :)

Okay, I just checked in a small change to Pattern.py in the prosite
parser (search() in regular expressions was complaining if you passed
None as the endpos parameter) and that seemed to make the prosite tests
happy. So, right now only prodoc and gobase are failing, which I think
(hopefully) is the expected failure rate right now. I think I'm going to
stick with 2.0 since it is pretty snazzy, so I'll keep my eyes open :-).

Brad