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

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

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


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
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Attachment #1072 is|0                           |1
           obsolete|                            |




------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-21 06:59 EST -------
(From update of attachment 1072)
Hi Cymon,

I've just checked in something based on your patches:

Checking in BioSQL/Loader.py;
/home/repository/biopython/biopython/BioSQL/Loader.py,v  <--  Loader.py
new revision: 1.37; previous revision: 1.36
done
Checking in BioSQL/BioSeq.py;
/home/repository/biopython/biopython/BioSQL/BioSeq.py,v  <--  BioSeq.py
new revision: 1.31; previous revision: 1.30
done
Checking in Tests/test_BioSQL_SeqIO.py;
/home/repository/biopython/biopython/Tests/test_BioSQL_SeqIO.py,v  <-- 
test_BioSQL_SeqIO.py
new revision: 1.27; previous revision: 1.26
done

This should fix the strand, feature db ref in locations, and importantly the
start/end with sub-features.

I am avoiding the ontology question by leaving location.term_id as NULL
(following BioPerl usage).

I'd like to do the same with location_qualifier_value.term_id but the schema
does not allow NULL here.  Interestingly BioPerl does not seem to use this
table, so I assume they (like Biopython) have been assuming "join".

I think this is still a big improvement, but that the
(sub)feature.location_operator issue could wait.  We'll need to discuss on the
BioSQL mailing list how this should be handled consistently.

Leaving this bug open.


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