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

[Peter Cock]

On Mon, Nov 26, 2012 at 4:46 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> Done,
> https://github.com/biopython/biopython/commit/9f6e810cc68dd1e353d899772fda3053d9f49513
>
>>> 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.
>>
>> Yes.
>
> Started, it seems the two _index.py files have diverged a
> little more than I'd expected:
> https://github.com/biopython/biopython/commit/ad1786b99afd2a50248246d877ff00a53949546b

I've just refactored the code in order to avoid most of the
index duplication (including SQLite backend) between the
SeqIO and new SearchIO index and index_db functions.

In the short term at least, the common code is now part
of Bio/File.py (but remains as private classes). That
seemed neater than introducing a new private module.

Fingers crossed everything is fine on the buildslaves,
TravisCI seems happy. Bow, if you find I've broken
anything then we need more unit tests ;)

Regards,

Peter