[Biopython-dev] Population Genetics code

Tiago Antão tiagoantao at gmail.com
Fri Dec 22 18:19:26 UTC 2006


During the last few months I have developed a lot of code in Python
around the topic of Population Genetics. Things from parsers (GenePop,
fdist2, Arlequin), to invoking other programs (simcoal2, fdist2), to
statistics (Fst, expected heterozygosity, ...), to data structures
representing population relationships, to HapMap data analysis,
currently I am developing code to interact with UCSC table browser...
Some of this code is used from Jython, by the way.

I am now in the process of consolidating the mess that I have done (I
have sometimes, several implementations of the same thing, just
because I was too lazy to do proper reuse). I was thinking that I
could do that in the context of BioPython, ie contributing the code.
Especially because BioPython seems to lack Population Genetics code.

Code quality varies a lot, from highly tested - under heavy use, to
one offs that were used a single time. But, even things that are poor
quality can easily be upgraded. The biggest issue is that some code
dealing with representation of molecular markers is still not matured
enough, ie, I believe that even good code it will have change quite a
lot in the future, breaking interfaces...

Anyway, I was thinking in starting with an easy task, namely
converting my parsers of GenePop and fdist2 to BioPython. These are 2
absolutely trivial formats.

Any comments on this? Would there be an interest in population
genetics oriented code?


The right to offend is far more important than the right not to be
offended - Rowan Atkinson

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