[Biopython-dev] [Bug 2833] Features insertion on previous bioentry_id

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed May 20 20:25:39 UTC 2009


------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2009-05-20 16:25 EST -------
(In reply to comment #0)
> Biopython 1.50 (also 1.50b it's the same code)
> python2.4 or python2.5
> postgresql 8.3
> BioSQL Schema 1.0.1
> Problem: 
>  imagine to have 3 seqrecord (s1,s2,s3), ... load a Biosql db in this order:
>  - db.load([s1])
>  - db.load([s2])
>  - db.load([s3])
>  At the end of the loading i will have only 2 bioentry ID 
>  BUT the s3.features will be inserted on s2 seqrecord.

BioSQL will allow you to have multiple versions of the same record but they
must have different versions (e.g. s1.id="ENST00000334859.0" and
s3.id="ENST00000334859.1" should work). The problem with your data is s1.id ==
s3.id, so I would expect them to get the same accession and version (taken as
zero).  Therefore s3 should *fail* to load.

I can try and reproduce this using the information given, but it would help if
you could attach the original sequence files to this bug.



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