[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 #40 from bsouthey at gmail.com  2008-11-06 09:24 EST -------
(In reply to comment #38)
> (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"?
> 

I think to_end because end does mean the end of the translation due to a stop
codon or end of a sequence.


> > b) from_start_codon=True (or init=True etc) if there are no valid start codons
> 
> As written in attachment 1032 [details], if the sequence does not start with a valid
> start codon an exception is raised.
> 

Okay.


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