[Bioperl-l] Bio::Coordinate::GeneMapper cds to peptide bug

[Aaron Mackey]

On Thu, May 13, 2010 at 2:20 AM, Heikki Lehvaslaiho <
heikki.lehvaslaiho at gmail.com> wrote:

>
> As of getting values outseide the defined region, that is a feature rather
> than a bug. The idea was to be able to ask what would the new coordinate be
> if the feature extended beyond the known limits. The is the capability of
> Bio::Coordinate::ExtrapolatingPair that is used here. That class also has a
> method strict that can be used to prevent extrapolating, but the code to
> access that has not been written into GeneMapper. I'll see if I can get it
> to work.
>
>
I had this same thought/expectation, but that in fact is not what's going
on.  There is no place in the GeneMapper code where the CDS end coordinate
is being used, only the begin coordinate.  The implicit assumption is that
the CDS ends at the last exon.

>From the perspective of the translate/revtranslate methods, an extrapolating
pair does not make sense (at least to me) -- just as a CDS coordinate is
undefined within an intron, so too would I expect a CDS coordinate to be
undefined in an UTR or intragenic region.

Alternatively, it would be nice (in general) to be able to check whether the
provided mapping is an extrapolation or not.

-Aaron