[Biopython] IUPAC code contribution

[Eric Talevich]

On Mon, Jun 6, 2011 at 6:18 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> On Mon, Jun 6, 2011 at 10:52 PM, Michal <mictadlo at gmail.com> wrote:
> > Hello,
> > I would like to contribute the following IUPAC function to Biopython:
> >
> > def iupac_base(alignment):
> >    IUPAC = {
> >      ord('N'): 'N',
> >      ord('G'): 'G',
> >      ord('A'): 'A',
> >      ord('T'): 'T',
> >      ord('C'): 'C',
> >      ord('G') + ord('A'): 'R',
> >      ord('T') + ord('C'): 'Y',
> >      ord('A') + ord('C'): 'M',
> >      ord('G') + ord('T'): 'K',
> >      ord('G') + ord('C'): 'S',
> >      ord('A') + ord('T'): 'W',
> >      ord('A') + ord('C') + ord('T'): 'H',
> >      ord('G') + ord('T') + ord('C'): 'B',
> >      ord('G') + ord('C') + ord('A'): 'V',
> >      ord('G') + ord('A') + ord('T'): 'D',
> >      ord('G') + ord('A') + ord('T') + ord('C'): 'N'}
> >
> >    return IUPAC[sum(map(ord, {}.fromkeys(alignment).keys()))]
> >
> >
> > a = iupac_base(['A','A','T','T','T'])
> >
> > Cheers,
> > Michal
>
> Well it would need some documentation at least (e.g. a docstring).
> What is is meant to do? It looks like you just want a reverse lookup
> of Bio.Data.IUPACData.ambiguous_dna_values - e.g.
>
> from Bio.Data.IUPACData import ambiguous_dna_values
> rev_map = dict((frozenset(v),k) for (k,v) in
> ambiguous_dna_values.iteritems())
> assert rev_map[frozenset('CG')] == rev_map[frozenset('GC')]
>
>
This is also a good candidate for a Cookbook entry on the Biopython wiki:
http://biopython.org/wiki/Category:Cookbook

Then others can easily comment on it, describe use cases and suggest
alternatives.

-Eric