[BioPython] calculate F-Statistics from SNP data

[Giovanni Marco Dall'Olio]

On Mon, Oct 20, 2008 at 3:57 PM, Giovanni Marco Dall'Olio <
dalloliogm at gmail.com> wrote:

>
>
> On Mon, Oct 20, 2008 at 7:41 AM, Tiago Antão <tiagoantao at gmail.com> wrote:
>
>> Hi,
>>
>> On Sun, Oct 19, 2008 at 3:50 PM, Giovanni Marco Dall'Olio
>> <dalloliogm at gmail.com> wrote:
>> > ok, thank you very much!!
>> > I would like to use git to keep track of the changes I will make to the
>> > code.
>> > What do you think if I'll upload it to http://github.com and then
>> upload it
>> > back on biopython when it is finished?
>> > I am not sure, but I think it would be possible to convert the logs back
>> to
>> > cvs to reintegrate the changes in biopython.
>>
>> I think it is a good idea. When we reintegrate back I think there will
>> be no need to backport the commit logs anyway.
>
>
> Ok, I have uploaded the code to:
> - http://github.com/dalloliogm/biopython---popgen
>

I wrote a prototype for a PED file parser which uses your PopGen.Record
object to store data.
It's available on github: I have still to finish the consumer object and to
test it, but I think I will be able to finish it for today.

I left you a few comments on the github wiki:
- http://github.com/dalloliogm/biopython---popgen/wikis/home

Maybe the biggest issue is that I will have to use this library to parse
very big files, so there are a few things we could change in the
implementation of the parser.
Is there any way in python to force the interpreter to store variables in
temporary files instead of RAM memory?
I was thinking about modules like shelve, cPickle, but I am not sure they
work in this way.
We could also modify the parser in a way that it can accept a list of
populations as argument, and create a populations list with only those
populations from the file.

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My Blog on Bioinformatics (italian): http://bioinfoblog.it