[Biopython-dev] [Bug 1963] Adding __str__ method to codon tables and translators

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1963





------- Comment #2 from mdehoon at ims.u-tokyo.ac.jp  2007-01-27 18:01 -------
> Question One:
> Is this worth adding to BioPython or not?

Yes, definitely.

> Question Two:
> What is the preferred behaviour for ambiguous tables?  Just a 4x4x4 table as
> for the unambiguous tables?  Or the full 15x15x15 table?  I have implemented
> both (see commented out code)

My feeling is that 15x15x15 would become too large to be clearly visible on the
screen. So I'd prefer 4x4x4, maybe with a reminder printed at the end as to
what each ambiguous codon may represent.

> Question Three:
> Is there a standard BioPython function to convert from one letter amino acid
> sequences into three letter names?  i.e. like one_to_three from
> Bio.PDB.Polypeptide but more general.  That function does not cope with
> ambigous names.

There is the function seq3 in Bio/SeqUtils. If it is not complete, it can be
extended easily, and seems to be a better place for this general function than
Bio/PDB/Polypeptide.


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