[Bioperl-l] lightweight features

Chris Fields cjfields at uiuc.edu
Wed Nov 7 20:04:05 EST 2007


I'm also thinking a factory is a good possibility; maybe something to  
take the place of FTHelper.

chris

On Nov 7, 2007, at 5:19 PM, Hilmar Lapp wrote:

> 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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>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>
>
>
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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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