[Bioperl-l] BPlite as SeqAnalyisParserI

[Ewan Birney]

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
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