[BioPython] calculate F-Statistics from SNP data

[Peter]

On Thu, Oct 16, 2008 at 11:02 AM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> Hi,
> I was going to write a python program to calculate Fst statistics from a
> sample of SNP data.  Is there any module already available to do that
> in biopython, that I am missing?  I saw there is a 'PopGen' module, but
> the Cookbook says it doesn't support sequence data.
> Is someone actually writing any module in python to calculate such
> statistics?

I think this will be a question for Tiago (the Bio.PopGen author),
although others on the list may have also tackled similar questions.

In terms of reading in the SNP data, what file format will you be
loading?  Does Bio.SeqIO currently suffice?

Have you looked into what (if any) additional python libraries you
would need?  For any Biopython addition, a dependency on just numpy
that would be preferable, but Tiago has previously suggested an
optional dependency on scipy for additional statistics needed in
population genetics.

Peter