[Biopython-dev] Working with the new SearchIO API

Kai Blin kai.blin at biotech.uni-tuebingen.de
Thu Nov 1 09:10:11 UTC 2012

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.


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
D-72076 Tübingen                        Fax :   ++49 7071 29-5979
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben

More information about the Biopython-dev mailing list