[BioPython] calculate F-Statistics from SNP data

[Tiago Antão]

Hi,

On Wed, Oct 22, 2008 at 11:25 AM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
> I wrote a prototype for a PED file parser which uses your PopGen.Record
> object to store data.

Don't feel obliged to use GenePop.Record. You can (maybe you should)
use one that is better for your PED record. The point is: your PED
files might have extra (or less) information than genepop files. For
instance, they might have population names. They might store the SNP
(A, C, T, G). With genepop you would have to convert (and thus loose)
the extra info.

> Maybe the biggest issue is that I will have to use this library to parse
> very big files, so there are a few things we could change in the
> implementation of the parser.

Yet another reason to develop your own record. I would not mind
helping you with that.

> We could also modify the parser in a way that it can accept a list of
> populations as argument, and create a populations list with only those
> populations from the file.

We have to be careful in modifying existing code. We can add new
functionality, add new interfaces. But changing existing interfaces or
removing them has to be dealt with exceptional care, because that will
break (existing) code done by users.

Tiago