[Biopython-dev] PopGen code

Peter biopython-dev at maubp.freeserve.co.uk
Fri Jan 12 12:36:56 UTC 2007

Tiago Antão wrote:
> Hi,
> A couple of weeks ago I have put on bugzilla code related to
> population genetics, namely parsing of GenePop and Fdist files, plus
> code to control fdist.
> I have had no feedback whatsoever, namely comments to the quality of
> the code, if there is interest in adding it in the future to
> BioPython, etc...
> I have much more code that I could start converting to BioPython
> format, some of which is a bit more complicated to convert (e.g., an
> Arlequin format parser). Before I start doing it I would like to know
> if there will be any feedback at all or if I am just loosing my
> time...

I suppose I/we would be able to read your code from a general 
perspective (coding style, clarity of comments, etc).  I haven't made 
time for this.

I suspect BioPython currently has no active developers who feel 
qualified to interpret your population genetics code.  I was hoping that 
you and Ralph Haygood would combine forces - if you are both happy with 
some code that does bode well.  Any comments Michiel?

Regarding population genetic file formats - from a very quick search 
about Arlequin it sounds like this file format can hold lots of 
different types of data.  I would encourage you to try and come up with 
a generic population record data object that could hold this or 
information from GenePop or Fdist as well.  I have no idea how easy this 
would be...


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