[Biopython] sequence coordinate mapping

[Peter]

On Fri, Jun 18, 2010 at 7:00 PM, Reece Hart <reece at berkeley.edu> wrote:
> Thanks, all, for feedback. I'm still digesting some of the previous
> comments. For the purposes of discussion, I've attached the crude
> (pre-crude, even) implementation that I mentioned.

Thanks

> Caveats/ToDos:
> * The interface is sufficient for my needs, but for a large number of CDS
> subfeatures, it might make sense to change the implementation index
> rather than linear search.

It looks like the core idea you are using is the same - loop over the exons
(subfeatures) to keep track of where you are.

> * I ignore strand for the moment.

That makes like a bit more fun! I haven't tested my code on mixed
strand features yet (e.g. some crazy tRNA annotation I've seen).

> * I don't use SeqFeature.AbstractPosition and friends.

Unfortunately they crop up in lots of real world GenBank/EMBL files,
so anything we add to the SeqFeature object has to cope with them.
Things like GFF3 files avoid this of course.

Peter