[BioPython] codons and complements

[Kate]

----- Original Message -----
From: Jeffrey Chang <jchang@SMI.Stanford.EDU>
> > So: maybe just the simple "translate" (read past stop codons, use
> > standard-or-passed-code-table, do _no_ check for modulu 3) should be a
> > method.
>
> These defaults seem reasonable to me.
>
>
> > My proposal: translate is a method, special translates are user-written
> > functions.
>
> I'm still a little bit uncomfortable with this.  Translating a sequence
> with the wrong genetic code would be meaningless.  Thus, having a
> translate method on a sequence object implies that the genetic code should
> be carried around as well.  This may be superfluous to people's use of the
> object, or at worst, unnecessarily force someone to look up the proper
> code for the sequence to preserve the semantics of the object.
>
   Maybe we should post a user survey form and solicit user feedback.  The
survey could have type of instititution, job description of the user,
organisms studied, ultimate goal of the research, etc. Then we could  use
the feedback to develop prototypical use scenaries.

  Like
         Professor Myco
        Works for a startup drug research firm.
         Searches fungus DNA for cheap versions of current cancer drugs.

    etc.

   And base our decisions on the most likely scenarios.


Cayte