[Biopython-dev] New Biopython release coming up / Alphabets

Frank Kauff fkauff at duke.edu
Thu Jul 6 17:53:23 UTC 2006

On Thu, 2006-07-06 at 12:39 -0400, Michiel Jan Laurens de Hoon wrote:
> Michael Hoffman wrote:
> > [Peter]
> >> But to be honest, I have generally used plain strings in my own
> >> programs, and meddled with alphabets only when needed (e.g. for
> >> translating from DNA to protein sequences).
> Note that there is a function "translate" in Bio.Seq that translates DNA 
> to protein using plain strings.
> > 
> > I agree. In general, I think that the alphabet stuff adds unnecessary
> > complexity to perhaps 95 % of the sort of things I would do with
> > Biopython. But as it stands I usually use strs myself instead.
> It appears that most people (myself included) use plain strings instead 
> of Seq objects (= string + Alphabet). We should check on the biopython 
> mailing list if anybody really needs alphabets, and if not get rid of 
> them (after the upcoming Brooklyn-release (1.42) though).
I use seq objects and the alphabet stuff in the nexus parser, but I
don't really know why and wouldn't mind at all to get rid of them. 


> --Michiel.
Frank Kauff
Dept. of Biology
Duke University
Box 90338
Durham, NC 27708

Phone 919-660-7382
Fax 919-660-7293
Web http://www.lutzonilab.net

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