[Bioperl-l] lightweight sequence features

Chris Fields cjfields at uiuc.edu
Tue Nov 6 16:57:17 EST 2007


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




More information about the Bioperl-l mailing list