[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


mmokrejs at ribosome.natur.cuni.cz changed:

           What    |Removed                     |Added
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                 CC|                            |mmokrejs at ribosome.natur.cuni
                   |                            |.cz




------- Comment #6 from mmokrejs at ribosome.natur.cuni.cz  2008-07-18 20:37 EST -------
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.


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