[Bioperl-l] lightweight sequence features

Jason Stajich jason at bioperl.org
Tue Nov 6 23:14:55 EST 2007


Right - only for simple locations.  I've got a bunch more tests and  
fixes to put in.

I am hoping this can be fast replacement in the case where we're  
dealing with this "unflattened" data (i.e. GFF in FeatureIO &  
Gbrowse).  This is sort of a playground until I feel like it can  
really get  it tested a bit more.  I'll give an all clear when the  
dust settles in terms of the design if anyone wants to play/help.

-jason
On Nov 6, 2007, at 4:57 PM, Chris Fields wrote:

> Bravo!  I once benchmarked Location instance creation once and  
> found it contributed quite a bit of overhead so the speedup with  
> that and the use of arrays makes quite a bit of sense to me.
>
> You mention only simple locations; I'm guessing this doesn't handle  
> 'fuzzy' ends?  If it did I could see layering the feature data from  
> the get-go, so it could be used just about anywhere in the place of  
> SF::Generic.  Maybe something to test out in 1.7?
>
> chris
>
> On Nov 6, 2007, at 3:18 PM, Jason Stajich wrote:
>
>> I started a branch for implementing and playing with lightweight
>> feature object. The branch is called 'lightweight_feature_branch'.
>>
>> Right now it is about 70% faster just in object creation based on
>> parsing features using Bio::Tools::GFF and swapping the types of
>> features that are created.  It uses arrays instead of hashes under
>> the hood.
>>
>> So the objects don't have locations under the hood.  My hope is if
>> this works okay we could use it for creating objects where we KNOW
>> the underlying features have simple locations so such as parsing in
>> GFF data.
>>
>> -jason
>> --
>> Jason Stajich
>> jason at bioperl.org
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>



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