[Bioperl-l] (no subject)

Jason Stajich jason at bioperl.org
Wed Nov 7 14:52:16 EST 2007


The array-based Bio::SeqFeature::Slim is only about 7% faster than  
Bio::Graphics::Feature so I suspect most of the speedup comes from  
removing location objects.

Generic     6.75        --      -37%      -41%
GraphicsF   4.26       58%        --       -7%
Slim        3.98       70%        7%        --

this is using code on the lightweight_feature_branch so
cvs -d:ext:USERNAME at pub.open-bio.org:/home/repository/bioperl co -r  
lightweight_feature_branch -d core_lwf bioperl-live

http://jason.open-bio.org/~jason/bioperl/seqfeature_speed.pl
and the GFF3 file I used to parse
http://jason.open-bio.org/~jason/bioperl/sgd.gff3.bz2

-jason


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