[BioPython] calculate F-Statistics from SNP data

[Giovanni Marco Dall'Olio]

On Wed, Oct 22, 2008 at 6:00 PM, Tiago Antão <tiagoantao at gmail.com> wrote:

> 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.


I first tried to write an AbstractPopRecord class from which to derive both
Ped.Record and your GenePop.Record classes.
Then, I realized that I wanted to use all of your methods and decided to
import your GenePop.Record instead of writing a new one.
Moreover, there are some methods (like GenePop.Record.split_in_pops) that
create Record objects, and I thought it would have been easier to always
refer to the same one.
Maybe we should write a generic PopGenRecord in which to store all general
informations about population genetics data.


>
>
> > 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
>



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