[Biopython-dev] Working with the new SearchIO API

[Wibowo Arindrarto]

Hi Kai,

You're welcome :). I was thinking changing Hit similar to QueryResult,
which you can create without containing any items. The trade off is that
there's more attributes to keep track of (4 instead of 2) due to them being
stored apart from the contained objects, so I chose not to do it for now.

Anyway, let me know if there are still parsing difficulties because of the
object model.

cheers,
Bow


On Thu, Nov 1, 2012 at 10:10 AM, Kai Blin <kai.blin at biotech.uni-tuebingen.de
> wrote:

> On 2012-11-01 09:19, Wibowo Arindrarto wrote:
>
> Hi Bow,
>
> > 2. Regarding the Hit object API change, I've changed it so that Hit
> > objects can now be created without any HSPs
> > (
> https://github.com/bow/biopython/commit/e9137c9ed88c09f6e488f50184292cac474327c4
> ).
> > However, per my explanation about keeping as few places possible to
> > store the same value (in this case the hit and query ID and
> > description), the empty Hit object will raise errors if any of these
> > attributes are accessed. Setting and getting these attributes will
> > only work if there is at least one HSP in the Hit. Other Hit
> > functions, like append, should work ok as long as it doesn't involve
> > accessing these attributes. I think this will allow parsing of file
> > formats like HMMER2 plain text while maintaining the attribute storage
> > constraint.
>
> I totally agree the Hit object isn't valid until it has at least one
> HSP. Thanks for that change.
>
> Cheers,
> Kai
>
> --
> Dipl.-Inform. Kai Blin         kai.blin at biotech.uni-tuebingen.de
> Institute for Microbiology and Infection Medicine
> Division of Microbiology/Biotechnology
> Eberhard-Karls-University of Tübingen
> Auf der Morgenstelle 28                 Phone : ++49 7071 29-78841
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>