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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Jul 19 12:52:02 UTC 2008


------- Comment #8 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-19 08:52 EST -------
(In reply to comment #6)
> I was just about to report this bug. I use biopython to translate EST
> sequences. They are full of sequencing errors although one knows the CDS
> region, still it is often interrupted by N's or by literal STOP codons. The
> current implementation in biopython-1.47 broke it for me. I haven't tested the
> attached patches but would propose to make this strict check optional.
> Currently it seems there is no way to pass down the code some variable not to
> barf in such cases. Will attach my current hack.

Do you have an example which "worked" in an older version of Biopython, but is
"broken" in Biopython 1.47?

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