Subject: Re: Slowness of Bioperl with GFF3 database access
Date: Tuesday 4th December 2012 20:53:08 UTC (over 4 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 Sjøgren in certain critical bottlenecks. And as many [email protected] programmers have observed since, one is very often mistaken about where these bottlenecks are."