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Issues With Biosql And Biopython--Can'T Access Features And Annotation

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

biopython
• 2,085 views • link
written by dtomso • dtomso

2 answers

Duplicate of this mailing list thread: http://lists.open-bio.org/pipermail/biopython/2013-March/008387.html

• 10 views • link
written by Peter Peter

Oops, apologies, didn't mean to spam too many sources.

Also--issue is resolved by latest github update of BioPython, no explanation yet for mechanism.

Thanks!

• 0 views • link
written by dtomso • dtomso

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