[Biopython-dev] RNA Alphabet: request for comments

Peter biopython at maubp.freeserve.co.uk
Wed Jun 16 08:51:03 UTC 2010

On Wed, Jun 16, 2010 at 9:32 AM, Kristian Rother <krother at rubor.de> wrote:
> Hi Peter,
>> Why not create a Seq subclass instead of your class ModifiedRNAString(str)?
> This turned out to be a lot simpler. Worked right away. New commit at:
> http://github.com/krother/biopython/commit/b0a6071f2b08a4f9bfee33a8d675c0e21b60ba70
> more comments welcome.

Why do you need the  _set_sequence method? Why not just put that
small piece of code inside the __init__ method?

> Next steps from my side would be:
> 1) add all modifications to the Alphabet.
> 2) add some RNA-specific methods.
> 3) add more tests.
> 4) sync with latest master branch.
> 5) request code merge.
> Best regards,
>     Kristian

If this works out we should look at doing a Protein 3-letter code version
for use with PDB sequences (I'm thinking about the modified amino acids).


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