[Biopython-dev] FDist: more Population Genetics code

Ralph Haygood rhaygood at duke.edu
Wed Jul 11 03:45:56 UTC 2007

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.


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

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