[Bioperl-l] Frame translation gets an extra aa?

Karger, Amir akarger at CGR.Harvard.edu
Wed Jan 19 17:36:02 UTC 2011

> From: Chris Fields [mailto:cjfields at illinois.edu]
> I wrote: 
> > there should be
> some way to do either assuming or not assuming without too much
> extra work.... the extra object copying
> might be a problem if you were trying to write fast code, which
> luckily I'm not in this case.
> Fast code and BioPerl?  We're trying to make things faster, but
> this may be more difficult in practice with the default OO system
> (and a complete switch to Moose will be problematic in the short
> term).
> I have committed a fix to github for the above.  Basically, setting
> either '-complete' or '-complete_codons' will fill out partial
> codons and attempt to translate them, but this behavior is off by
> default.  I think this makes sense, just from the perspective we
> don't want unintended side-effects.

That makes sense to me. The truth is, there shouldn't be that many real life applications, as far as I can tell, where this bites people meaningfully. But having the option is nice.


More information about the Bioperl-l mailing list