[Biopython] Indexing large sequence files

[Peter]

On Tue, Jun 23, 2009 at 10:14 PM, Cedar McKay<cmckay at u.washington.edu> wrote:
>
> I gave your code a shot, and it worked great! My script took 13 minutes to
> run, which is a lot better than before, when it would die from lack of
> memory. Thanks a lot!
>
> Cedar

Great :)

Was it the FASTA only version, or the more generic one you tried?
(I would expect the times to be about the same from my limited
benchmarking).

Did you have an old version of the script using Bio.Fasta.index_file
from Biopython 1.43? How long did that take?

Peter