[Biopython-dev] GenePop parser code

Tiago Antão tiagoantao at gmail.com
Thu Dec 28 00:11:22 UTC 2006


On 12/27/06, Peter (BioPython Dev) <biopython-dev at maubp.freeserve.co.uk> wrote:
> That sounds sensible - unless there is some generic object structure you
> want to introduce for handling population data?  I don't know enough
> about this to comment.

Well, this has been floating around my mind... In fact I would need to
introduce, sooner or later, notions like population, individual,
marker... What I currently have is enough for me, but I am pretty much
aware that its not generic enough. One good example of this is Ralph
Haygood's messages that you talk about, where he uses mainly sequence
data statistics (I work more with SNP and microsatellite data), as
such I suppose my data structures would not be enough for his work
(and vice-versa).
I propose the following strategy:
1. I will try to contact him (maybe he still reads this list? Are you
there? ;) )
2. I will have a much more closer look at Bio::PopGen from BioPerl.
3. Wait for any more comments on this list
Let see where this leads to...

In the mean time I have some less problematic code: mainly code to
work with Mark Beaumont's fdist program, parser and code to control
it. The problem here is that fdist is such a niche program, that I
don't think it deserves to be at top level Bio (but my suggestion is
for it to be supported, as is clearly used in population genetics). I
think it would make more sense to be Bio.PopGen.FDist rather than
Bio.FDist, just to not to make Bio too "noisy". Does this make sense?

PS - Tomorrow I will submit GenePop code as you suggested

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

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