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

[Eric Talevich]

On Fri, Mar 2, 2012 at 9:02 AM, James Casbon <casbon at gmail.com> wrote:

> On 1 March 2012 18:30, Eric Talevich <eric.talevich at gmail.com> wrote:
> > 2012/3/1 Peter Cock <p.j.a.cock at googlemail.com>
> >> 2012/3/1 Eric Talevich <eric.talevich at gmail.com>:
> >> > Variants
> >> > --------
> >> >
> >> > So, from the Biopython 1.60 thread:
> >> >
> >> > - James Casbon has offered to merge PyVCF into Biopython, right?
> >> > - BCF, the binary form of VCF (via blocked gzip), may also
> >> >   be worthwhile to support
> >> > - GVF, the Genome Variation Format, appears to be intended
> >> >   to be competitive with VCF. It's probably at least as well
> >> >   thought-out as VCF, sight unseen. It's based on GFF.
> >> >
> >> > 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?
> >>
> >
> > Does someone feel comfortable asking James for his thoughts on this?
> >
> > I'm not especially well qualified to mentor this, though I could assist
> as
> > a secondary mentor if needed. Any other Biopython devs/users well
> > acquainted with VCF/PyVCF?
>
> I'm willing to co-mentor this.
>
> I would think the easiest route would be to initially add bcf support,
> then GVF.
>

Thanks for volunteering, James! I've added your name to the list of mentors
on the wiki page:
biopython.org/wiki/Google_Summer_of_Code