[Biopython-dev] SearchIO, was: PEP8 lower case module names?

[Peter Cock]

On Mon, Nov 26, 2012 at 1:49 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> Once that's done there is some housekeeping to do, like
> the indexing code duplication with Bio.SeqIO, and tackling
> indexing BGZF compressed files with Bio.SearchIO which
> I will have a go at.
>

I've started work on SearchIO indexing of BGZF files now,
enabling it was quite simple (the same code as used for
SeqIO the indexing):
https://github.com/biopython/biopython/commit/cf063bf6a2dca4d534d00699310548e43bf2e14f

Thus far I've only tested this with BLAST XML, but that did
require a bit of reworking to avoid doing file offset arithmetic:
https://github.com/biopython/biopython/commit/600b231a1817035141c8de80e5689dcfd31290b5

I will resume this work later this afternoon, going over all
the SearchIO file formats one by one.

Regards,

Peter