[Bioperl-l] SeqIO profiling

[Ewan Birney]

On Sun, 22 Sep 2002, Jason Stajich wrote:

> oops - was working on seqfeature collection for my own stuff - meant to
> say annotation collection.
> 
> Speaking of Seqfeature::Collection - my idea is to eventually shoehorn
> this more robust object for feature collections into the Bio::Seq system -
> this would allow Bio::Seq to be-a Bio::DasI compliant and essentially do
> Das from a genbank file.  But one could use the original array-based
> methods to not pay any more performance costs.  Since you can't really
> store objects in DB_File structures, what I do instead is store array
> locations in a DB_Tree B-TREE which can then be used to extract certain
> features from the feature array.
> 
> The interface for SeqFeature::Collection should be hammered into Bio::DasI
> shape before 1.2 IMHO.  Something I meant to do this summer but never got
> around to....

I look into this. THe idea is that Bio::Seq has-a
Bio::SeqFeature::Collection which is-a Bio::DasI compliant object right?




> 
> -jason
> 
> On Sun, 22 Sep 2002, Hilmar Lapp wrote:
> 
> >
> > On Sunday, September 22, 2002, at 02:23 PM, Ewan Birney wrote:
> >
> > > On Sun, 22 Sep 2002, Jason Stajich wrote:
> > >
> > >
> > >
> > >>
> > >> Additionally I just made the seqfeature collection instantiation
> > >> lazy so
> > >> it is only built when requested in Bio::Seq.  Don't think we'll
> > >> see much
> > >> improvement but would be good to test how much effect it had on fasta
> > >> format sequence parsing.
> > >>
> > >
> > >
> > > I wanted to do the same thing with the Bio::AnnotationCollection
> > > instantion as well...
> >
> > That's what Jason did -- Bio::Seq doesn't use SeqFeature::Collection
> > yet ... (hmm ... should it do so?)
> >
> > 	-hilmar
> > --
> > -------------------------------------------------------------
> > Hilmar Lapp                            email: lapp at gnf.org
> > GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> > -------------------------------------------------------------
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> 
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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