[Biopython-dev] Working with the new SearchIO API

[Wibowo Arindrarto]

Hi Kai,

> I've just stumbled over a case where not being able to pre-create Hit
> objects really bites me.
>
> See the attached hmmpfam output. You'll notice that the domain table
> is not in the order of the hit table. As I'd like to preserve the
> order of the hit table, the current setup of the API forces me to
> either repeatedly parse the domain annotations until I find the
> correct domain annotations for my hit, or to create the hits in the
> order of the domain annotation table and then reshuffle them to make
> sure they're in the order of the hit table.
>
> If I could just create "empty" hit objects when parsing the hit table,
> I could easily preserve the order of the hits but still add the hsps
> as I parse them.

Hmm..

This is a problem :/. I didn't expect any format to have this kind of ordering.

I'll see what I can do with the current API limitation. We may need to
change it back to not requiring any HSPs for Hit. In any case, I'll
see what needs to be done first and get back asap.

cheers,
Bow