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

[Dan Tomso]

Thanks, Peter.

I don't have the files, but I pulled them just the other day via BioPython
Entrez methods.
Here are several identifiers that I just verified (as having the problem):
384448934
121612099
384117894
229587578

Basically, I pulled these down, loaded them into the DB, and can (sort of)
retrieve the records, but when the records try to load up the annotations
or features, things fall apart.

I'll try to work up some comments on install.  There was at least one SQL
term that I needed to search and replace to get things to fly with the
latest MySQL.

Dan T.



On Mon, Mar 4, 2013 at 3:52 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> 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
>