[Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2530


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

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




------- Comment #14 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-08 11:25 EST -------
(In reply to comment #13)
> If there is agreement that changing the behaviour of Bio.Seq.translate() as
> described in Bug 2547 is desirable, then we end up fixing both issues at the
> same time.

I think an agreement was reached.  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

I dare say the implementation might be improved or optimised, but I think this
is a good improvement for the functionality.


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.