[Bioperl-l] Slowness of Bioperl with GFF3 database access

[Adam Sjøgren]

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."