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

[Dan Tomso]

Sure, will do.

DT

On Mar 4, 2013, at 3:59 PM, Peter Cock <p.j.a.cock at googlemail.com> wrote:

> On Mon, Mar 4, 2013 at 8:52 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.
>>> 
>>> ...
>>> 
>>> 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).
> 
> Based on the trace above, you could be running Biopython 1.60, but
> if you were running the current release of Biopython 1.61 you'd get
> a slightly more explicit TypeError here when there is something odd
> about the start co-ordinate.
> 
> Right now my hunch is a low level C int vs long issue, which could
> be dependent on the OS and MySQL version, and thus escaped
> our testing. If I'm right, this should be an easy fix.
> 
> Could you update to Biopython 1.61 (or the latest code from GitHub)
> and retest?
> 
> Thanks,
> 
> Peter