[Biopython] Issues with BioSQL and BioPython--can't access features and annotation

[Peter Cock]

On Mon, Mar 4, 2013 at 8:44 PM, Dan Tomso <dtomso at agbiome.com> wrote:
> Hi all--
> New list subscriber here.  I'm having an issue using DBSeqRecord objects
> pulled via BioSQL.  Any insight welcome!
>
> Hello all-- Running on Ubuntu 12.10 with Python 2.7, latest BioPython and
> BioSQL.
>
> I have successfully established the MySQL-based BioSQL server, and I can
> load sequences into the system properly (or they seem to be proper--tables
> are populated correctly in MySQL and things are generally error-free).

Excellent. That should have been the hardest part done. Any feedback on
how to improve the docs would be good - presumably you used this?:
http://biopython.org/wiki/BioSQL

> However--when I retrieve via 'lookup,' I can only access the id, name, and
> description for the DBSeqRecords. Annotations and features are supposed to
> be called on demand, but this crashes things. For example:
>
> File "/usr/lib/pymodules/python2.7/Bio/SeqRecord.py", line 595, in __str__
>     lines.append("Number of features: %i" % len(self.features))
>   File "/usr/lib/pymodules/python2.7/BioSQL/BioSeq.py", line 516, in
> __get_features
>     self._primary_id)
>   File "/usr/lib/pymodules/python2.7/BioSQL/BioSeq.py", line 280, in
> _retrieve_features
>     feature.location = SeqFeature.FeatureLocation(start, end)
>   File "/usr/lib/pymodules/python2.7/Bio/SeqFeature.py", line 561, in
> __init__
>     raise TypeError(start)
> TypeError: 0
> Any idea what is happening here? Thanks! Dan

Hmm. Do you have the original sequence file loaded into the database?
If so, we could try and reproduce the problem - that would be the
easiest way forward. Otherwise you might need to look into the
start value for the location for that feature (e.g. SQL queries on the
database, or some debug print statements in the Biopython code).

Thanks,

Peter