Revisited... Re: [Bioperl-l] Request for direction...

Mark Wilkinson
Tue, 16 Oct 2001 10:00:04 -0600

Malcolm Cook wrote:

> I recommend creating, say, Bio::SemanticFeatureInterpreter::Interface as a
> class of objects which programmatically 'edit' Bio::SeqI or
> Bio::Seq::RichSeq (or Bio::LiveSeq?) objects.  The nature of the edit could
> be arbitrary.  Objects which conform to the interface would implement a
> method named, say, 'interpret', which would take the seq and implement some
> systematic change to it.

I like this idea very much!  I think this is the route that I will take, rather
than making the interpretation a method of the Seq object as I had originally

This still leaves open the question of re-using exons (i.e. creating/not new
Exon objects for each transcript that includes a particular exon)...(and just
by the way I worded that statement you can already see my bias!  :-) )

I would prefer to have a single collection of exons, from which individual
exons are  designated as belonging to one or more Transcript objects.  This is
certainly the way I think about the biology of the process, and is also more
memory efficient as it is non-redundant.


If we have SemanticFeatureInterpreters, as suggested above, then we can have
the best of both worlds:  one interpreter which removes redundancies in its
gene models, and another which does not.

Does that sound like too much duplication of effort?

Anyone with a vested interest in the outcome please drop me a line.  I wont be
getting stuck into this project again for a couple of weeks as there is a fair
bit of cleaning up to do before Dave leaves our group to move on to greener
(and warmer) pastures in San Diego - congratulations Dave!!  I hope to be
working on it intensively in the first week of November.

Cheers all!


"Speed is subsittute fo accurancy."

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK