[Biopython-dev] [Bug 2838] If a SeqRecord containing Genbank information is read from BioSQL, it cannot be written to another BioSQL database

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri May 22 22:58:24 UTC 2009


------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-22 18:58 EST -------
(In reply to comment #0)
> I've been trying to annotate some microbial sequences; some are from genbank.
> So the proposed series of events was:
> 1) get sequences from genbank
> 2) store in BioSQL database called One
> 3) recover them from BioSql
> 4) annotate the recovered SeqRecords [this works, but isn't
>    necessary for this problem to be reproduced - here, I'm
>    making no changes at all to the SeqRecord]
> 5) store the annotated SeqRecords in a different BioSQL database called Two.
> The problem is that Step 5 fails when the original record was recovered from
> Genbank.
> The traceback (below) indicates a problem with the BioSQL loader in 
> _load_bioentry_date
> ...
> I'm a novice with Python and Biopython so please accept my apologies if
> there is something obvious and very stupid responsible for this.

What you are trying to do sounds very reasonable (although I have never
actually needed to or tried to do this myself). You were right about the date
thing, the loader code only expected a string, not a list. Fixed in CVS
revision 1.40 of BioSQL/Loader.py, and I have also added a unit test for this
use case in Tests/test_BioSQL.py revision 1.36.

Note there is a known minor discrepancy with dates (see Bug 2681) when
comparing the original SeqRecord to the DBSeqRecord after loading/retrieving
from BioSQL.

If you could confirm this solves your problem, I think we can close this bug.
Thank you!


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