[Bioperl-l] lightweight sequence features
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?
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 Stajich
> jason at bioperl.org
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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