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

[Wibowo Arindrarto]

Hi Peter,

>>>> 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.

Thanks :). I remember I did change some of the variable names. Other
than this, the biggest change is probably related to the Indexer
classes lazy loading in SearchIO. But it seems to have been handled as
well :).

> 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.

Looks like a good place for now, Bio.File as the location for common
file-handling code.

> 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 ;)

Will keep that in mind :).

regards,
Bow