[Biopython-dev] [Bug 2840] When a record has been loaded from BioSQL, trying to save it to another database fails with loader db_loader.load_seqrecord in _load_reference

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2840





------- Comment #9 from david.wyllie at ndm.ox.ac.uk  2009-06-04 17:59 EST -------
thank you very much for fixing this. 

I can confirm that in the current git load (4 june 09) the problem is resolved.

David

(In reply to comment #6)
> Hi David,
> 
> I was able to reproduce this problem. When working on Bug 2838, as my test case
> I was using just the file cor6_6.gb which by chance has simple reference
> locations - and that worked. I have now tested with GI 28804743. Also, using
> some of the other GenBank files in our test suites also shows the reference
> location problem from BioSQL/Loader.py function _load_reference:
> 
> ValueError: invalid literal for int() with base 10: 'None'
> 
> This is now fixed in CVS, plus there are now additional unit tests.  For the
> fix, I have used a slight variation of Cymon's patch. Does this look sensible
> Cymon?
> 
> BioSQL/BioSeq.py revision: 1.37
> Tests/test_BioSQL.py revision: 1.39
> Tests/seq_tests_common.py revision: 1.2
> 
> If you could retest with a clean checkout from CVS/github, to confirm the
> problem is fixed, that would be great David.
> 
> Note - currently in BioSQL we only store one reference location, while GenBank
> files can have a single reference covering multiple regions of the record. This
> is a limitation of the current BioSQL schema (although it would be interesting
> to see how BioPerl deals with this).
> 
> Note - there are four known failures in test_BioSQL.py right now, a mixed
> strand feature in NC_000932.gb (which triggers two failures), the project cross
> reference in NC_005816.gb, and a sub-feature location reference in one_of.gb --
> these are all unrelated to this issue (Bug 2840).
> 
> Thanks,
> 
> Peter
> 


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