[Biopython-dev] BioSQL Loader.py patch

Leighton Pritchard lpritc at scri.sari.ac.uk
Tue Apr 4 13:39:20 UTC 2006

Hi all,

I'm not sure if you want this here, or on the BioPython BugZilla, but
I've written a patch that modifies BioSQL/Loader.py to load db_xref
qualifier/value pairs, and also contains a patch to correct bug 1921
caused by the attempted default insertion of an invalid taxon_id.
The .diff is attached.  I've been living with the patched code for a
month without any issues, so it's been stable as far as I've needed it
to be (and has worked with all bacterial GenBank .gbk files and the
BioPython GenBank parser).

There are two sections of the patched code that print/write to stdout.
Is this an acceptable way of reporting to the user in a BioPython style?



Dr Leighton Pritchard AMRSC
D131, Plant-Pathogen Interactions, Scottish Crop Research Institute
Invergowrie, Dundee, Scotland, DD2 5DA, UK
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