[BioPython] PopGen module for Biopython?

[Alex Lancaster]

>>>>> "RH" == Ralph Haygood  writes:

RH> Fellow Biopythoneers, I'm a population geneticist (currently
RH> working at Duke University).  Since last spring, I've written a
RH> Python module for computing a variety of population-genetic
RH> statistics from DNA sequences, including popular favorites such as
RH> Tajima's D, Fu and Li's D, and Fay and Wu's H.  It can compute
RH> statistics for a whole alignment, or it can slide a window along
RH> an alignment, or it can compare a pair of congruent alignments
RH> (e.g., transcription factor binding sites versus other sites in a
RH> cis-regulatory region).  It runs under Biopython, in that it works
RH> on Bio.Align.Generic.Alignment objects.

Ralph,

On related population genetic tools in Python, I have a project that
uses Python, but is not yet integrated to use biopython, but I would
like to explore ways that it could do so.

PyPop: Python for Population Genetics:

http://www.pypop.org/

It currently does analyses such as (1) conformity to Hardy-Weinberg
expectations, (2) tests for balancing or directional selection; (3)
estimates of haplotype frequencies (and their distributions) and
measures and tests of significance for linkage disequilibrium (LD).
It's licensed using the GNU GPL.

It would be nice to integrate these tools, or somehow be able to
access them via biopython, and PyPop doesn't do the tests that you are
proposing, it would be nice to somehow integrate them also with your
tools.  (Some of the tests mentioned above are computationally
extensive and therefore are written in C, and are accessed from Python
using SWIG).

Way back in 2001, I posted to this list a query about standardising
input files for population data, but I guess that there weren't that
many pop. gen folks using biopython back then!

http://portal.open-bio.org/pipermail/biopython/2001-September/000723.html

Anyway, thoughts on this would be appreciated.

Alex
--
Alex Lancaster | Dept. of Integrative Biology, UC Berkeley: ib.berkeley.edu