[Bioperl-l] (no subject)

Chris Fields cjfields at uiuc.edu
Wed Nov 7 16:12:35 EST 2007


I can see preferring a lightweight simple SF over SF::Generic in the  
next BioPerl dev cycle.  I guess we would just layer split locations  
as simple sub-features/segments, typing when necessary?  That  
shouldn't be much more overhead than creating a layered Location::Split.

chris

On Nov 7, 2007, at 2:09 PM, Jason Stajich wrote:

> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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