[Biopython] Issues with BioSQL and BioPython--can't access features and annotation
Dan Tomso
dtomso at agbiome.com
Mon Mar 4 20:44:20 UTC 2013
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).
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
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