[Biopython-dev] [Bug 2677] BioSQL seqfeature enhancements

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2677





------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-20 05:17 EST -------
(In reply to comment #0)
> Cleaned-up (sub-)seqFeature locations, and strand. Added location_operator
> storage and test. Added remote location storage for sub-features, and test.
>

Excellent - I see you've removed the naive min/max to find the parent feature's
location when dealing with sub-features.  This should fix the special case
where a feature spans the origin on a circular genome.

That should take care of many of my "TODO" entries in test_BioSQL_SeqIO.py :)

>
> Ive used the "Sequence Keys" ontology for the location operator and stored
> loc op in the location_qualifier_value table - not sure this is right...
>

I'm not sure off hand either, but would like us to check before committing
this.  In the short term, what ever BioPerl does is "right" as I'm treating
that as the BioSQL reference implementation.

> 
> Patches attached.
>

I've scanned over them quickly, and they look fine.  The comments do help :)


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