[Biopython-dev] Population Genetics code

[Tiago Antão]

Hi!

Firstly I would like to thank everybody that answered so positively to
my "rant" about submitting population genetics code to Biopython.

I have a few suggestions on how to progress in a safe in constructive
way with a possible Population Genetics part for biopython.
First of all, the starting point:
1. There is none in the core developers that is working actively in
populations genetics
2. Point 1 entails that any code submissions (made by biopython
newbies like me) will not be able to be completely reviewed by
seasoned biopython developers
3. Initially there will only be me submitting code (please correct me
if I am wrong, especially Ralph...)
4. There is already some popgen statistical code in python lying
around e.g. http://www.pypop.org/

Therefore I suggest starting out by doing a small, "safe", project
around a not very used application (Mark Beaumont's Fdist program
http://www.rubic.rdg.ac.uk/~mab/software.html ). This code is already
done and tested (by myself). I also have test cases (in BioPython
format) for parts of it. The major issue is that it is currently
outside of Bio.PopGen namespace, so its not really very major...
I would provide parsers, configuration file generators and utilities
to run the suite of fdist programs.
Why start with such a simple and less relevant application:
1. Its safer to start with something less grand (if its poorly done it
won't be that serious).
2. There is no python fdist code lying around, so there is no overlap
at all with existing projects
3. This code is already done and being used...

I will provide code, test code, and documentation (probably by adding
stuff to the wiki). Then other people could evaluate what was done,
and we would continue from there to other, more used applications
(Genepop, arlequin, simcoal2, ...) and databases (HapMap,
TableBrowser).

Is this an acceptable way of going ahead? If other people would like
to participate, that would be fantastic...

If my suggestion is rubbish, please also say ;)

Many thanks,
Tiago