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

[Mark Wilkinson]

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
planned.

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.

BUT!!

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!

M


--
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"Speed is subsittute fo accurancy."
________________________________

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