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

Peter biopython at maubp.freeserve.co.uk
Wed Jun 9 12:53:39 UTC 2010

On Wed, Jun 9, 2010 at 1:28 PM, Laurent <lgautier at gmail.com> wrote:
> What about having a class instance instead ? This would let one change the
> index storage system very easily.

That is essentially what the recent code on my branch is doing, but
the back end isn't being exposed to the public API (yet).

> The this would be a call like:
> Bio.SeqIO.index(keyval_map = KeyValSQLite("myindex.db"))
> Now that you have the idea, getting a custom index based on BDB or
> anything should be a breeze...

Indeed. Most DB like back ends should offset a bulk loader we can
exploit via the dict's update method.


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