[Biopython-dev] Storing Bio.SeqIO.index() offsets in SQLite

Peter biopython at maubp.freeserve.co.uk
Tue Jun 8 09:35:15 UTC 2010

On Mon, Jun 7, 2010 at 10:10 PM, Kevin Jacobs wrote:
> On Mon, Jun 7, 2010 at 2:23 PM, Peter wrote:
>> Having now tried using this on some files with tens of millions of
>> records, tuning how we use SQLite is going to be important.
> Wouldn't a Berkeley database be much much faster for constructing
> simple key to offset mappings?

Maybe - now that I've done the refactoring on Bio.SeqIO.index() to
allow two back ends (python dict or SQLite) trying a third (BDB) is
much easier. Did you know BDB was used in the old OBDA index
files? However, Python 2.6 deprecated bsddb (the Python Interface
to Berkeley DB library) and Python is pushing people to SQLite3


More information about the Biopython-dev mailing list