[BioPython] Alphabet Checking

[Peter Cock]

> Aren't those two exactly equal?
>
> Matching references doesn't seem to work as expected :(

That does look like a bug...

> The only way around I was able to find is:

Another option,

from Bio import Translate
from Bio import Seq

trans=Translate.ambiguous_dna_by_id[11]
a=Seq.Seq("ATCGGATGAATGCAGT",alphabet=trans.table.nucleotide_alphabet)
print trans.translate_to_stop(a)
print trans.translate(a)

> I guess this is a bad day :( it's the second clash with the Translate
> module in the same day :|

I don't like the Bio.Translate module either.

> Should I report this as bug?

Please do.  If we do just add translation to the seq object (bug 2381)
and deprecate the Bio.Translate module then in a sense this problem
goes away ;)

Peter