Re: Slowness of Bioperl with GFF3 database access

On Wed, 28 Nov 2012 02:27:16 -0800 (PST), Francesco wrote:

> I'm experiencing that when I have to do a lot of accessess on a GFF
> database (with Bio:DB::SeqFeature::Store) the slowness increase until
> my script can stay running for more than a day.

First you'll need to find out what/where exactly it is slow. One way to
do so is using a a profiler; this is a good one for Perl:

 * https://metacpan.org/module/Devel::NYTProf

If you want more specific suggestions, you'll probably have to provide
more information.

  Good luck!

    Adam

--

-- 
 "As Knuth pointed out long ago, speed only matters           Adam Sjøgren
  in certain critical bottlenecks. And as many           asjo <at> koldfront.dk
  programmers have observed since, one is very often
  mistaken about where these bottlenecks are."