[Bioperl-l] (no subject)

Lincoln Stein lstein at cshl.edu
Wed Nov 7 15:04:24 EST 2007


I wonder if it is worth moving to the array-based version more generally,
then.

How does the array based feature object deal with tags?

Lincoln

On Nov 7, 2007 2:52 PM, Jason Stajich <jason at bioperl.org> wrote:

> 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<http://jason.open-bio.org/%7Ejason/bioperl/seqfeature_speed.pl>
> and the GFF3 file I used to parse
> http://jason.open-bio.org/~jason/bioperl/sgd.gff3.bz2<http://jason.open-bio.org/%7Ejason/bioperl/sgd.gff3.bz2>
>
> -jason
>



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Lincoln D. Stein
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