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Gmane
From: Adam =?iso-8859-1?Q?Sj=F8gren?= <asjo <at> koldfront.dk>
Subject: Re: Slowness of Bioperl with GFF3 database access
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Tuesday 4th December 2012 20:53:08 UTC (over 3 years ago)
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 Sj√łgren
  in certain critical bottlenecks. And as many           [email protected]
  programmers have observed since, one is very often
  mistaken about where these bottlenecks are."
 
CD: 3ms