[Biopython-dev] RNA Alphabet with modified nucleotides

[Kristian Rother]

Hi,

finally got some more tests and cleanup done on Bio.RNA.RNASeq. The
current branch

http://github.com/krother/biopython/commits/rna_alphabet

contains:
- doctests
- unit tests
- copyright statements
- added RNASeq object to test_Seq_obs.py
- compatibility to the Seq class
  (there is a caveat though: functions like
complement/translate/reverse_complement don't make sense on sequences
containing modified nucleotides, and result in an exception.)

Also, there is a branch with ongoing bugfix work on the PDB GSOC code, but
I need to correspond with Joao Rodrigues on this.

Best Regards,
   Kristian





Am 2010-07-01 15:26, Peter wrote:
> 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
>