[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





------- Comment #11 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-19 16:24 EST -------
How did you do the six translations in comment 9?  Using Bio.Seq.translate()
would have failed with a TranslationError on any "NNN" codon or similar.

By common agreement "*" is used for a stop symbol.  While "X" generally means
any amino acid, I have somethimes seen it used to mean any amino acid OR a stop
codon (in the NCBI translations in certain GenBank files).

Personally I think it would be nice if there was an agreed character for an
amino acid OR stop codon (e.g. "!" for example).  However, as far as I know no
such convention exists, so we shouldn't invent one as the default in Biopython.

P.S. The nicest way to handle translate("NNN") isn't what I filed this bug
about.  Its the fact that translate("{@}") or anything else like that returns
"*" and not an error.


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