[BioSQL-l] Loading SwissProt to BioSQL?

[Nathan Edwards]

What is the current recommended solution for those wanting to load 
SwissProt database files (uniprot_sprot.dat) to BioSQL via BioPython?

As far as I can tell, the situtation is this:

* The SwissProt .dat file parsers under Bio.SwissProt.SProt don't 
produce SeqRecord objects required by BioSeqDatabase.load.

* The SwissProt .dat file parsers under FormatIO can't parse SwissProt 
.dat files, period.

Does *anyone* have a working SwissProt .dat file to BioSQL solution 
working in Python?

The most recent solution I see suggested:

http://biopython.org/pipermail/biopython/2004-May/002088.html

doesn't work as advertised: SProt.SequenceParser produces SeqRecord 
objects with only minimal instantiation of SeqRecord fields (sequence 
and accession) and BioSeqDatabase dies because it expects a field that 
SequenceParser never instantiates; and FormatIO.readFile doesn't 
recognize the uniprot_sprot.dat as any format it recognizes, and if 
forced, with format='swissprot/38' or format='swissprot/40' it dies 
while parsing.

Note: My entire BioPython, BioSQL, etc installation is new, pristine, 
the latest update from CVS.

Thanks,

nathan

-- 
Nathan Edwards, Ph.D.
Center for Bioinformatics and Computational Biology
3119 Agriculture/Life Sciences Surge Building #296
University of Maryland, College Park, MD 20742-3360
Phone: +1 301-405-9901
Email: nedwards at umiacs.umd.edu
WWWeb: http://www.umiacs.umd.edu/~nedwards