[Bioperl-l] new_fast methods
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
> 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?
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.
More information about the Bioperl-l