DBSeqRecord cannot access annotations, features using BioSQL under BioPython - biopython

Question

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).
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?

Answer 1

I encountered the same error just this week.
A feature's start and end positions are retrieved from MySQL as type long (not int) but SeqFeature.py expects int only for start and end when instantiating a FeatureLocation. I don't know what has changed in mysql server, MySQLdb, BioSeqDatabase or SeqFeature to have provoked the problem.
Hopefully one of the biopython developers will be able to provide a long term solution but these are suggestions for temporary fixes:
try to get to the MySQLdb connection used by BioSeqDatabase and change the conversion behaviour with the conv keyword parameter of its connect function (I haven't been able to do this)
hack BioSeqDatabase so that start_pos and end_pos are converted to int after the values are fetched from MySQL (I haven't done this)
hack SeqFeature.py to allow long type for start and end when instantiating a FeatureLocation object (this is what I have done). Change this:
if isinstance(start, AbstractPosition):
self._start = start
elif isinstance(start, int):
self._start = ExactPosition(start)
else:
raise TypeError(start)
if isinstance(end, AbstractPosition):
self._end = end
elif isinstance(end, int):
self._end = ExactPosition(end)
else:
raise TypeError(end)
to this:
if isinstance(start, AbstractPosition):
self._start = start
elif isinstance(start, int) or isinstance(start, long):
self._start = ExactPosition(start)
else:
raise TypeError(start)
if isinstance(end, AbstractPosition):
self._end = end
elif isinstance(end, int) or isinstance(end, long):
self._end = ExactPosition(end)
else:
raise TypeError(end)