[BioPython] Clustalw multiple alignment

[Brad Chapman]

Hello all;
	I have been doing some work where I wanted to be able to interact
with the clustalw multiple alignment program. Basically, what I wanted to
do was to be able to set up a command line for clustalw, run clustalw,
parse the results and manipulate these result, all from within python.

So I wrote up some code which does the following stuff:

1. Provides a class to model the clustalw command line so that you can
set parameters you want from python.

2. Parses clustal formatted files (with *.aln extensions) using Martel
(Andrew's latest version) into a class which holds the sequences as
SeqRecord objects, and can write the alignment back out in the clustal
format.

3. Has some convenience functions to run clustal and parse the results
all in one shot.

4. Does a quick calculation of a consensus sequence from a bunch of
aligned objects.

I put the code for this at:

http://www.bioinformatics.org/bradstuff/bp/align.tar.gz

I was wondering if people had time to take a look at this and give me
feedback on it. I would like to also do something similar for pairwise
alignment code (any suggestions for existing C code to use?) so that I
could quickly compare two sequences and get an alignment score between
them.

The kind of feedback I am interested in is:

1. Is this kind of code useful to anyone besides me?

2. Do the interfaces make sense? How can they be improved?

3. Do you see any bugs, etc?

Thanks for listening, and enjoy!

Brad