[Biopython-dev] [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)

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http://bugzilla.open-bio.org/show_bug.cgi?id=2381





------- Comment #38 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-05 17:12 EST -------
(In reply to comment #36)
> (In reply to comment #35)
> Okay, this is what I think of the main uses for translation.
> All these can be easily achieved by the translate arguments
> table='Standard' and stop_symbol='*' with very little code.
> So I do not see any need for any extra arguments except
> for convenience. (I have these uses in file that I will
> upload after this.)

Most of your examples seem to relate to open reading frame searches, looking
for start/stop codons etc.  I agree this kind of thing isn't needed in the
basic translate method/function.

Doing a CDS translation however is more fiddly due to the methionine at the
start, and I think this warrents another option in the basic translate
method/function.

> So really my only issue left is what is the expected behaviour for:
> a) to_stop_codon=True if there are no valid stop codons (my understanding of
> to_stop).

If you are asking about the current to_stop argument in CVS right now, if there
is no in frame stop codon it will translate all the sequence (to_stop has no
effect).  I've just updated the docstring to make this more explicit (see
Bio/Seq.py CVS revision 1.55).

Do you think "to_stop_codon" is a clearer argument name than "to_stop"?

> b) from_start_codon=True (or init=True etc) if there are no valid start codons

As written in attachment 1032, if the sequence does not start with a valid
start codon an exception is raised.


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