[Bioperl-l] new_fast methods

Jason Stajich jason at bioperl.org
Fri Feb 27 13:40:21 EST 2009


it is probably deservedly ignored until I actually get around to  
figuring out how I'll add it back in -- I can put it in bioperl-dev -  
that is a good idea, will try and remember to move when I get a little  
time.

On Feb 26, 2009, at 11:00 AM, Chris Fields wrote:

> 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

Jason Stajich
jason at bioperl.org





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