[Biopython-dev] BioSQL upgrade [0 of 3]

Brad Chapman chapmanb at arches.uga.edu
Sun Nov 24 15:26:38 EST 2002


> Here's a set of patches to update BioSQL.  It:

Sweet. Thanks much for this work! I've got it all checked in and tests
pass on both Postgres and MySQL on my machine. I also checked a current
biosqldb-mysql.sql and biosqldb-pg.sql into Tests/BioSQL so the Tests
looks for them there -- this way we have the SQL that we know works in
the test directory and all that kind of good stuff.

Just one note on your implementations. In a lot of the SQL strings you
used %d when an integer was expected in the schema. This seems to work
fine in Postgres but MySQLdb craps out on it, complaining with a
TypeError about an integer being needed. To solve this, everything
should just be %s in the SQL string and then all the necessary magic
just takes place -- this works with both databases.

> [2] Bio.SeqRecord.SeqRecord
> I believe this means in practice a GenBank record, as SProt uses another 
> class.

Yup, I implemented this "generic" SeqRecord class when I did the
GenBank stuff, and SwissProt was already finished at that time. Ideally,
parsing into SeqRecords should be supported for everything, but it just
hasn't been done yet.

Thanks again for all this work! Hopefully I've got everything into CVS
okay -- let me know if anything seems wonky or anything.


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