[Biocorba-l] SeqFeature -> get_Primary_Seq

[Jason Stajich]

On Thu, 8 Feb 2001, Ewan Birney wrote:

> On Thu, 8 Feb 2001, Matthew Pocock wrote:
> 
> > > The SeqFeature interface includes a method 'seq_primary_id()' that returns
> > > the primary identifier for the Seq that this SeqFeature belongs to.
> > > 
> > > For a little while longer, I'm going to continue my crusade for SeqFeature
> > > to be naive about the actual sequence from whence it came outside the
> > > range of the feature (other than via a primary identifier!)  :)
> > > 
> > > 
> > > cheers,
> > > alan
> > 
> > An understandable view - solves issues with circular references & object 
> > ownership for naive implementations. Do bioperl features hold references 
> > to their 'containing' sequences?

We don't require a reference to the containing sequence in the interface,
but in the main implementation (Bio::SeqFeature::Generic) when a 
feature is attached to a Seq object it stores a reference to the Seq
object and we have a method seq() which will return the
subseq for this SeqFeature from the start/end boundaries as defined by the
SeqFeature.  So that is really the reason I asked in the first place
because I can use this seq method if we only want to obtain the sequence
as bounded by the SeqFeature object.  If we want the whole PrimarySeq back
I'll need to add another method to Bio::SeqFeature::Generic to return the 
whole thing.

> Nope. This difference between Bio::Seq and Bio::PrimarySeq (PrimarySeq's
> don't have features, features have a link to PrimarySeq's).
> 
> I find this a good model.
> 
> 
> > 
> > Just to give my ID crusade - they are of no meaning without knowing 
> > which database to look them up in - the tuple {ID, SeqDB} is what is 
> > realy required if you use ID at all. Also, there is the issue of wether 
> > resolving the ID gives you back a CORBA object that is equivalent or 
> > identical.
> > 
> > Matthew
> > 
> > _______________________________________________
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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/