[Biopython-dev] genetic code

[Peter Cock]

On Tuesday, December 11, 2012, Lenna Peterson wrote:

> Hi Matthias,
>
> In a similar case, we have a file in the Scripts/ directory to download and
> parse the file. The generated file (and not the source file) is committed,
> but the script is available in the source for end users who wish to update
> it:
>
>
> https://github.com/biopython/biopython/blob/master/Scripts/PDB/generate_three_to_one_dict.py
>
> I think a similar situation would be appropriate here. Does Biopython
> currently include alternate codon tables?
>
> Cheers,
>
> Lenna


Yes, see
https://github.com/biopython/biopython/blob/master/Bio/Data/CodonTable.pyon
the parser therein.

On Tuesday, December 11, 2012, Matthias Bernt wrote:
>
> > Dear biopython developers,
> >
> > there is a new genetic code table (24) in the NCBI resources (see
> > NC_015649). Maybe you can update this with the next release.


That seems like a Good idea :)


> > Would it be an idea to distribute the genetic code file from ncbi with
> > biopython and create the code tables on import or during installation?
> Then
> > biopython would be automatically up-to-date.
> >
> > Regards,
> > Matthias
>

That would just make installation more complex (and it is already
complicated). I would prefer to keep setup.py as normal as possible.

The NCBI tables rarely change, so this works OK overall.

Peter