[Biopython-dev] RNA Alphabet with modified nucleotides

[Peter]

On Thu, Jul 1, 2010 at 2:01 PM, Kristian Rother <krother at rubor.de> wrote:
>
> Hi,
>
> I've commited code + tests for representing RNA sequences with modified
> nucleotides to a branch on Github. See:
>
> http://github.com/krother/biopython/commits/rna_alphabet
>
> I'm done with my list of 'most wanted' features for this class, including
> suggestions from Peter.
> What could I do next to help integrating the new code with the rest of
> Biopython?

Hi Kristian,

I haven't had a play with the code, just a very brief look at it.

You'll need to add licence and copyright statements.

A few embedded doctests in the docstrings would be very nice
to help explain how the new classes are to be used.

What happens if you add some of the new DNA seq objects
to test_Seq_objs.py? Is it all fine?

Are you planning to add a reverse complement method etc? Or
does the current fall back on the Seq implementation work OK?

Peter