[BioPython] Alphabet Checking
Peter Cock
p.j.a.cock at googlemail.com
Mon Jan 28 17:56:11 UTC 2008
> 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
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