[Bioperl-l] (no subject)

Jason Stajich jason at bioperl.org
Wed Nov 7 15:09:35 EST 2007


It uses hashes there so technically it is not entirely array based.

-jason
On Nov 7, 2007, at 3:04 PM, Lincoln Stein wrote:

> 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
>>
>
>
>
> -- 
> Lincoln D. Stein
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> FOR URGENT MESSAGES & SCHEDULING,
> PLEASE CONTACT MY ASSISTANT,
> SANDRA MICHELSEN, AT michelse at cshl.edu



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