[BioPython] Translation of ambiguous codons like NNN and TAN

[Peter]

Dear all,

I've recently filed Bug 2547 about changing the behaviour of
Bio.Seq.translate() when given ambiguous codons like NNN or TAN which
could be either an amino acid OR a stop codon.

http://bugzilla.open-bio.org/show_bug.cgi?id=2547

In my opinion it would be nice if there was an established convention
for how to represent an ambiguous character meaning {X or stop}, for
the TAN example even {Y or stop}.  However, as far as I am aware,
people just use X to mean any amino acid OR a stop codon.  This is the
behaviour in both the EMBOSS transeq tool and in BioPerl.

I am proposing to change Bio.Seq.translate() be able to translate
codons like NNN and TAN as X (rather than throwing a translation error
as happens now).

Comments please?

[Any implementation suggestions on the development mailing list please.]

Peter