[Biopython-dev] BGZF support, was Re: Biopython 1.60 plans and beyond

[Kevin Jacobs <jacobs@bioinformed.com>]

On Tue, Apr 17, 2012 at 11:23 AM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Sat, Feb 18, 2012 at 9:39 AM, Peter Cock <p.j.a.cock at googlemail.com>
> wrote:
> >
> > Here are some things that I think are strong
> > candidates for 1.60 (not an exclusive list!)
> >
> > ...
> >
> > BGZF support: Low level module like Python's gzip,
> > support in SeqIO for indexing BGZF compressed files,
> > ...
>
> I've just rebased my bgzf branch, which I think is ready to apply to the
> trunk. It has been tested under Python 2, PyPy [*], Jython and Python 3.
> https://github.com/peterjc/biopython/tree/bgzf2
>
> Would anyone like to review this please? There are unittests and
> plenty of docstrings - but so far nothing in the Tutorial though.
>
>
Hi Peter,

I've implemented code to create BAM/tabix style index files and perform
lookups, so it has been high on my list to test and validate your BGZF code
(rather having to write my own).  I'm notoriously short on time, but this
is in the critical path for several projects and I'm going to work on it
over the next week or so.

-Kevin