[Bioperl-l] new_fast methods

Chris Fields cjfields at illinois.edu
Thu Feb 26 11:00:12 EST 2009


On Feb 26, 2009, at 7:52 AM, Jason Stajich wrote:

> FYI - I wrote some lightweight feature objects - there is a branch  
> for it (lightweight_feature_branch) - these had a pretty significant  
> speedup.
>
> A lot of the overhead with sequence/feature/location creation since  
> there are so many objects being created, so optimizing these  
> features by using arrays instead of hashes for the data structure  
> seemed to provide a pretty significant speedup as well.  Ensembl  
> uses a fast_new as well, right?
> Bio::SeqFeature::Slim
>
> -jason

I have been working on a Bio::Seq::RichSeqI that essentially does a  
fast_new (simple bless) and is a lazy parser, e.g. parses files for  
seq record start/end only, then does everything else (annotation,  
features, etc) on the fly.  I'll probably be adding it to bioperl-dev  
sometime in the next few weeks.

Jason, did you want to move the lightweight implementation off the  
branch to bioperl-dev?  I worry about it getting ignored there.

chris


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