[Bioperl-l] Issue in Terminal Partial Codon Translation (1.6.0 ->1.6.1) ?

[Karger, Amir]

On 3/5/13 3:55 PM, "Chris Larsen" <clarsen at vecna.com> wrote:

>Hello BioPerl-l,
>
>A biologist might know that this terminus is always going to be a
>Glycine, G, since the third position is irrelevant, and so we would like
>to extend the partial codon into another amino acid in the last 'E2'
>protein encoded by this genome fragment. It's not sequenced but we can
>infer. The viral proteins are so short, it really matters! We want that G
>(and SPTAVRL). However the newer BioPerl version is not giving us the
>last amino acid. The functionality appears to be turned off, or a default
>argument was changed?  Issue with -complete ?
>
>
>
>PS: Chris F and Amir discuss : highly related issue:
>http://bioperl.org/pipermail/bioperl-l/2011-January/034401.html
>
>"why should CodonTable::translate() automatically 'complete' the
>translation for incomplete codons by default?  I would consider this a
>bug."

I guess one man's bug is another man's feature.

Sorry to have ruined your pipeline.

-Amir