[Biopython-dev] [Biopython] Update: call for Google Summer of Code project ideas

[Brad Chapman]

Peter and Eric;

> > Variants
> > --------
> > Synthesizing the above, we have a GSoC project that looks like:
> >
> > - Help merge PyVCF into Python (w/ James's support -- I
> >   don't mean to volunteer him for this in absentia)?
> > - Write a GVF parser that emits the same object type as
> >   PyVCF, potentially also using existing GFF code
> > - Time permitting, look into blocked gzip support for VCF
> >   (BCF), also looking at SAM/BAM for inspiration and
> >   reusable code.
> 
> Sounds interesting - who might be willing to mentor it?

This is a great idea. Reece and I proposed a variant project last year,
and Reece has already e-mailed me this year about trying again. He was
planning on re-vamping the description on the GSoC page for 2012:

http://biopython.org/wiki/Google_Summer_of_Code

so hopefully we can incorporate several aspects of this. From my
experience I would prioritize BCF/Tabix files since you see a lot of
those in practice.

For GVF we could certainly leverage the GFF parser since it is GFF with
variant keywords. Practically, I would love to settle on one format for
this and VCF seems to have the most tool uptake so far.

> >> SearchIO?
> >> ---------

+1 for this as well. Great ideas,
Brad