[Biopython-dev] Arlequin sequence files in Bio.Popgen

David Winter winda002 at student.otago.ac.nz
Sat Jul 18 08:17:02 UTC 2009

Hi again Tiago,

Sorry about falling of the grid before I could get back to you about this.

Tiago Antão wrote:
>>  I've uploaded my Arlequin classes and
>> functions to a branch on github so you can see them (/Bio/PopGen/Arlequin/
>> on http://github.com/dwinter/biopython/tree/arleq-branch)
> This is great, I took your code and created a new version (nothing
> more than also an initial sketch - Feel free to disagree/propose
> changes), you can find it here:
> http://github.com/tiagoantao/biopython/tree/arlequin

Yeah, all the changes you talk about seem sensible to me

> OK, somebody has to do a parser to actually read the files in ;) .
> Which is the biggest piece of work to be done. I don't mind doing it
> (like in the next month or so - I have some free time now), but you
> can do it if you want. In case you decide to do it, I have just one
> major point to note: making a parser that is able to read big files
> (i.e., some files cannot be parsed into memory in one go). I made this
> mistake with the genepop parser and some people do complain about it.
> Somethings cannot be read as lists to memory but have to be read as
> iterators (issue 3 above).
> I think a parser that is able to handle lots of files is also good to
> help in building a sound model to represent an arlequin record.
> As usual we will need test code and documentation for all this ;)

This is where I have to admit to not having the time or the skills to  
this justice, I'm happy to provide what help I can, (especially with  
the docs and tests which are probably closer to my skill-set) but just  
couldn't promise to do the bulk of the work.

There might also be another option, a bit of searching in github found this:


Open (MIT license) code for dealing with Arlequin in python. I'll  
contact the author and ask if he is interested in contributing (it  
can't hurt to ask right?)


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