[Biopython-dev] FDist: more Population Genetics code

[Tiago Antão]

Hi,

I had no feedback and it seemed that there was no interest, so I
decided to start a Python Population Genetics project on google, which
is going ahead, but still on alpha stages:
http://code.google.com/p/pypopgen/
I am doing this on a personal basis for now (I did not even announce
it anywhere), and so it is advancing at my personal pace and design
according to me needs
I have used it already (or a tiny part of it) on a published
aplication ( http://popgen.eu/soft/m4s2 ).
I am still willing to integrate this on BioPython, but for that some
interest and feedback would be needed... That would have to happen
somewhat soon as the code will have to be adapted to BioPython
standards and namespace, and when, in a future, there is a lot of code
that will be in practice difficult (and after going public it will be
impossible really).

The "strangest" code that I am doing (and that would need more
discussion) is one to do asyncronous computation (to be easy to use on
multicore computers and grids).

Regards,
Tiago

On 7/11/07, Ralph Haygood <rhaygood at duke.edu> wrote:
> Peter and Tiago,
>
> Hello.  No, I haven't done anything with Tiago's code.  I'm afraid
> it's pretty far from what I'm working on these days.
>
> I still think it would be good for BioPython to include methods for
> computing basic population-genetical statistics (Watterson's theta,
> Tajima's D, etc.) from DNA alignments.  I have in mind something like
> BioPerl's PopGen (http://www.bioperl.org/wiki/HOWTO:PopGen).  My own
> code is easy to use with a Bio.Align.Generic.Alignment, but it doesn't
> conform to BioPython's standards for style, testing, or documentation,
> and I don't know when I'll have time to standardize it.
>
> Ralph
>
> On Tue, 10 Jul 2007, Peter wrote:
>
> > Hi Tiago,
> >
> > Have you had any feedback (off the mailing list)?
> >
> > Ralph - did you have a chance to look over Tiago's code or discuss this with
> > him?
> >
> > It would be a shame if nothing came from this...
> >
> > Peter
> >
> > Tiago Antão wrote:
> >> Hi!
> >>
> >> I have submitted another enhancement bug, with support for FDist. It
> >> allows to generate and parse Fdist files and to control fdist
> >> applications. There are also a couple of utility functions. FDist is a
> >> niche application (mainly used to detect selection in animal
> >> genetics). Not the most fundamental one to support, but it is
> >> currently one that I am working on, thus, the code.
> >>
> >> Regarding my summited code for GenePop, I have summited a different
> >> version on bugzilla.  The main difference, is that I moved everything
> >> from Bio to Bio.PopGen.
> >>
> >> Before I continue putting code on bugzilla I would like to know if it
> >> is worthwhile doing it... Any opinions on the code submitted or if any
> >> changes are required? I would really like to continue converting my
> >> code to BioPython, but only if it has any possibility of ending up
> >> being useful/included in distribution somewhere in the future... ;)
> >>
> >> I am currently working on code related to SimCoal2, Arlequin and
> >> general statistics (Fst, heterozygosity, ...). Which will probably be
> >> ready quite soon (ie, next two weeks). This is more mainstream than
> >> FDist
> >>
> >> I have some other code lying around mainly related to HapMap, but I
> >> will only submit it after reviewing and reusing it again. This is more
> >> distant future ... like a couple of months.
> >>
> >> Tiago
> >
> >
> >