[Biopython-dev] FDist: more Population Genetics code

[Tiago Antão]

I just want to add that I followed precisely the procedure that I was
suggested at that time, ie to open bugzilla issues, but I got no
answer or follow up from it. I also had some very useful mail
exchanges with Ralph at that time, but no code was floated around.

I reiterate my interest in supplying the code (currently supporting
fdist, simcoal2, genepop, hapmap, ucsc table browser - in varying
degrees of quality). You can have a look at the google url supplied
(svn repository in it). I would still take the necessary time to
convert it to BioPython namespace and format.

If in one week I see no interest (interest in the form of pro actively
making things go forward) at all then I will consider this a closed
issue and will not spend more time with trying any form of
integration, in the sense that I have done all that was requested here
and really got no feedback.

Tiago

On 7/11/07, Tiago Antão <tiagoantao at gmail.com> wrote:
> 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
> > >
> > >
> > >
>