[BioPython] PopGen module for Biopython?

[Iddo Friedberg]

Hi Alex,

I already wrote Ralph regarding his contribution. I think the integration
idea is terrific, if it is appropriate, of course. I am not exactly sure
about the GPL licensing of pypop into software with the Biopython
license... maybe someone here can provide an answer.

Anyhow, let me know if you need any help on this. And if you want to
communicate more regarding pypop and Ralph's-yet-to-be-named package, it
will be great to do that in biopython-dev at biopython.org

Cheers,

Iddo

--
Iddo Friedberg, Ph.D.
Burnham Institute for Medical Research
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171
http://iddo-friedberg.org
http://BioFunctionPrediction.org

On Wed, 8 Feb 2006, Alex Lancaster wrote:

> >>>>> "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
> 
> 
> _______________________________________________
> BioPython mailing list  -  BioPython at biopython.org
> http://biopython.org/mailman/listinfo/biopython
>