[BioPython] Biopython and population genetics

[Jeffrey Chang]

>If not all of our code can be released, then at the very least,
>perhaps some of our modules could be contributed directly to biopython
>or be made as "optional" add-ons to biopython.

Yep, it would be really cool if your code could be released. 
However, getting permission to release code as open source can be 
difficult.  See the open source authors mailing list:
http://open-bio.org/mailman/listinfo/authors

>* suggestions about how such parsing modules might be most elegantly
>   integrated into the biopython framework;

The proper way to do it would be to create a subdirectory under Bio/ 
with a name that's descriptive of the data file.  There's an ad-hoc 
standard that parsers have a method called "parse" that takes a 
handle and returns some sort of object.

I don't work in population genetics, so will leave it to you and the 
community to find a good solution that's generalizable for others' 
needs.

Jeff