[Bioperl-l] BioPerl newbie question about exporting sub_SeqFe atures

[Gosink, Mark (SEA)]

Hello all,
	My 'real-use case' is that I would like to use multiple applications
to predict transmembrane regions. I would like to add all of the predicted
transmembrane regions from any single application as a single feature. The
actual transmembrane regions within the protein sequence would be
sub-features. True this may not be the most elegant of approaches but it
fits with the way I view the problem. It also allows me to keep any global
scoring and any local scoring as tags (such as generated by HMMer with
multidomain containing proteins).
Thanks for the fix and all your comments,
Mark
> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Tuesday, April 17, 2001 2:52 PM
> To: Jason Stajich
> Cc: Gosink, Mark (SEA); 'Hilmar Lapp'; 'bioperl-l@bioperl.org'
> Subject: RE: [Bioperl-l] BioPerl newbie question about exporting
> sub_SeqFe atures
> 
> 
> On Tue, 17 Apr 2001, Jason Stajich wrote:
> 
> > Problem is if you want to have a Feature A, and attach 
> Feature B and C
> > onto Feature A.  If you want to maintain a description for 
> B, C, how would
> > you do this?  add_sub_SeqFeature might have to get smarter 
> and translate
> > the contained Location object into a SplitLocation.
> 
> So this all comes down to "what do you mean" aka "how do you want this
> represented in EMBL/GenBank" and/or "how do you want other programmars
> access to your object". 
> 
> I think we've got to hear what Mark's real use case is, but 
> it wouldn't
> surprise me if the best solution is to inheriet off 
> SeqFeature::gneeric
> and overload to_FtHelper. Trying to make a one-size-fits-all 
> SeqFeature
> class without programming language extension is probably not going to
> work.
> 
> 
> (NB - we have the same problem with attributes getting muddled up with
> eac_tag_value semantics. This is just the inherent 
> polymorphism of feature
> objects and us trying to tame them with interfaces and - even more
> restrictive - data formats)
> 
>  > 
> > BTW: I think the 'EXPAND' way of adding features looks messy to me,
> > shouldn't all of this be captured in an object?
> > 
> 
> EXPAND is messy. My fault. I *think* that we should be 
> pointing people to
> the location object as the first place to solve this - in 
> fact, I would
> not be against removing add_sub_SeqFeatures from 
> SeqFeature::Generic and
> making sub_SeqFeatures return () but this might be a little 
> too dranconian
> here.
> 
> 
> This is all interesting grist to chew on as we encourage 
> people to build
> ontop of bioperl. I favour the sub-classing method, but it 
> does require
> programming expertise.  Hmmmm. Worth arguing about for sure.
> 
> 
> PS - about to watch the european footie now. 
> 
> 
> 
> 
> > -jason
> > 
> > On Tue, 17 Apr 2001, Ewan Birney wrote:
> > 
> > >
> > >
> > > Guys -
> > >
> > >
> > > the "real" bug here in some sense is that Mark is not using
> > > SplitLocations, and, in addition, that what "sub_SeqFeatures" mean
> > > relative to a Split Location is really ill defined, 
> and/or that the whole
> > > mapping of "complex object" to EMBL/GenBank is a ... 
> semantic mire.
> > >
> > >
> > > Mark - what do you actually want to do? It may wellbe 
> that you want to be
> > > introduced to the wonders of the to_FTHelper function 
> which will give you
> > > full control of the way your features is dumped in EMBL 
> and GenBank
> > > format.
> > >
> > >
> > >
> > > e.
> > >
> > >
> > >
> > > -----------------------------------------------------------------
> > > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > > <birney@ebi.ac.uk>.
> > > -----------------------------------------------------------------
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l@bioperl.org
> > > http://bioperl.org/mailman/listinfo/bioperl-l
> > >
> > 
> > Jason Stajich
> > jason@chg.mc.duke.edu
> > Center for Human Genetics
> > Duke University Medical Center
> > http://www.chg.duke.edu/
> > 
> > 
> > 
> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 


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