[Bioperl-l] BPlite as SeqAnalyisParserI

[Ewan Birney]

On Mon, 19 Feb 2001, Jason Stajich wrote:

> I'm just going to return the HSPs so that BPlite next_feature will keep
> track of the Sbjct and when it exhausts the current Sbjct of all of its
> nextHSP calls I'll try and get a new Sbjct, when there are no more Sbjcts
> to get then the next_feature will return undef.

This is the right way to go in my view....


> 
> This is the simpliest way to do this without major changes to the code,
> BPlite::Sbjct objects really don't hold any information other than the
> name of the query so it is useless to try and make them a SeqFeatureI.
> HSP contains all the relavent information so I'll just return HSPs.  It
> will be up to the user to interpret that some HSPs are attributed to
> different query seqs (by looking at hsp->query->seqname).
> 
> -jason
> 
> On Mon, 19 Feb 2001, Ewan Birney wrote:
> 
> > On Mon, 19 Feb 2001, Hilmar Lapp wrote:
> > 
> > > Jason Stajich wrote:
> > > > >
> > > > > I'm afraid at the same time I'll have to issue an exception permit
> > > > > for the SeqFeature::Gene stuff to settle down, and for BPlite
> > > > > (Jason, any chances?) to adopt the SeqAnalysisParserI interface.
> > > > > I'd still like to expire these permits Monday night.
> > > > 
> > > > Hmm, in order to do this, either we make Bio::Tools::BPlite::Sbjct a
> > > > SeqAnalysisParserI or we need to find a way to make a Sbjct a SeqFeatureI
> > > > which doesn't really make sense to me.
> > > > 
> > 
> > 
> > I had the smae problem in HMMER, which has a HMMSequence and a (badly
> > named) HMMUnit which is a featurepair.
> > 
> > I flattened the array of HMMSequence (each of which has an array HMMUnits)
> > to just an array of HMMUnits. 
> > 
> > 
> > This is what we do in the Ensembl "runnable" system as well, so it is a
> > tried and tested route...
> > 
> > 
> > 
> > 
> > > 
> > > The SeqAnalyisParserI is supposed to convert input into a stream
> > > of seqFeatures, so Sbjct cannot take that role. It should be
> > > possible to make Sbjct a SimilarityPair-derived object, which will
> > > make it a SeqFeatureI automatically. Check out
> > > Bio::SeqFeature::SimilarityPair::_fromBlastObj(), where I create a
> > > SimilarityPair object from a Blast::Sbjct object (or a Blast::HSP
> > > alternatively).
> > > 
> > > So, provided BPlite::Sbjct can be made to inherit off
> > > SimilarityPair, next_feature() in BPlite.pm would simply return
> > > one subject after another, until there are no more. If changing
> > > BPlite::Sbjct to inherit off SimilarityPair is too cumbersome,
> > > next_feature() could also grab the next BPlite::Sbjct object and
> > > create a SimilarityPair instance from its properties, much like
> > > SimilarityPair::_fromBlastObj() does it from a Blast::Sbjct.
> > > 
> > > Sounds okay? Am I missing something?
> > > 
> > > 	Hilmar
> > > -- 
> > > -----------------------------------------------------------------
> > > Hilmar Lapp                              email: hlapp@gmx.net
> > > GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
> > > -----------------------------------------------------------------
> > > _______________________________________________
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> > > 
> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>. 
> > -----------------------------------------------------------------
> > 
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> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> 
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-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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