[Bioperl-l] lightweight features

Hilmar Lapp hlapp at gmx.net
Wed Nov 7 18:19:15 EST 2007


It seems to me that there are applications where you're dealing with  
a huge number of features (such as GFF) and where therefore a  
lightweight object makes tremendous sense. But when you parse a  
genbank file, I'm not sure that's the bottleneck, unless maybe it's a  
large contig with lots of feature annotations.

I guess we'll ultimately want a way to control the type of feature  
being instantiated by a parser, e..g using a factory.

	-hilmar

On Nov 7, 2007, at 4:12 PM, Chris Fields wrote:

> 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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> Bioperl-l at lists.open-bio.org
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-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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