[Biopython-dev] [Bug 2547] Translation of ambiguous codons like NNN and TAN

[bugzilla-daemon at portal.open-bio.org]

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


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-08 11:23 EST -------
Bug 2530 and Bug 2457 are fixed in CVS as of Bio/Seq.py revision 1.37 (with the
unit test updated in test_seq.py revision 1.20).

Old behaviour (e.g. Biopython 1.48):

translate("TAT") -> "Y"
translate("TAG") -> "*"
translate("TAR") -> "*"
translate("TAN") -> TranslationError (Bug 2547)
translate("NNN") -> TranslationError (Bug 2547)
translate("TA?") -> "*" (Bug 2530)

New behaviour (CVS as things stand):

translate("TAT") -> "Y"
translate("TAG") -> "*"
translate("TAR") -> "*"
translate("TAN") -> "X"
translate("NNN") -> "X"
translate("TA?") -> TranslationError

Note that this new behaviour (translation of ambiguous possible stop codons)
could be made optional for backwards compatibility, but I would be surprised if
anyone would want the old behaviour.

Also, we could make the possible stop character an optional argument, but that
then brings up questions about how to represent this in the Alphabet objects.


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