[Biopython] Degenerated Codons

[Matthias Bernt]

hi peter,

Thank you for the suggestions. I will try to create the functions as
suggested.
Should I post them here?


> Where table could be ambiguous or unambiguous,
> DNA or RNA? Something like this works nicely for
> unambiguous tables:
>
> from Bio.Data.CodonTable import unambiguous_dna_by_id
> for table in [unambiguous_dna_by_id[1], unambiguous_dna_by_id[2]]:
>    print table.id
>    for codon in  ["AAA", "ATT"]:
>        amino = table.forward_table[codon]
>        alt_codons = [k for (k,v) in table.forward_table.iteritems()
> if v==amino]
>        print "%s -> %s, %i codons for this amino acid" % (codon,
> amino, len(alt_codons))
>
> Giving:
>
> 1
> AAA -> K, 2 codons for this amino acid
> ATT -> I, 3 codons for this amino acid
> 2
> AAA -> K, 2 codons for this amino acid
> ATT -> I, 2 codons for this amino acid
>
>
> > But maybe its possible to modify the backward_table such
> > that it stores all codons (as list) for a amino acid. For the other
> > functions building on it (back translation...) it would be possible
> > to take the first element of the list.
>
> We can't change that for backwards compatibility, but we
> could add a alt_backward_table or something instead
>

I think we keep it as it is at the moment. Performance is not so important
for me .. so far.
Optimisation can still be done later.

Matthias