[Biopython-dev] [Biopython] Exonerate Parser Error

[Lenna Peterson]

On Fri, Mar 21, 2014 at 3:32 PM, Zheng Ruan <zruan1991 at gmail.com> wrote:

> Hi Bow,
>
> I have the same problem when trying to model codon alignment with
> frameshift being considered. Basically, I have a CodonSeq object to store a
> coding sequence. The only difference between CodonSeq and Seq object is
> that CodonSeq has an attribute -- `rf_table` (reading frame table). It's
> actually a list of positions each codon starts with, so that translate()
> method will go through the list to translate codon into amino acid. In this
> case, it is easy to store a coding sequence with frameshift events. And
> it's not necessary to split the protein to dna alignment into multiple part
> when frameshift occurs. However, the problem now becomes how to obtain such
> information (`rf_table`). I find exonerate is quite capable of handling
> this task, especially with introns in the dna. I do think an object to
> store protein to dna alignment is necessary in this scenario.
>

Is the (still unmerged) CoordinateMapper the solution to this?
http://biopython.org/wiki/Coordinate_mapping
If so, let me know and I'll rebase and refresh the pull request.
If not, I misunderstood the problem.

Cheers,

Lenna