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

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

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





------- Comment #44 from bsouthey at gmail.com  2008-11-06 10:08 EST -------
(In reply to comment #42)
> Peter in comment #40
> >>> 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"?
> >>>
> 
> Bruce in comment #41:
> >> I think to_end because end does mean the end of the translation
> >> due to a stop codon or end of a sequence.
> >>
> 
> Leighton in comment #42: 
> > I would take 'to_end' to mean 'to the end of the passed sequence,
> > ignoring all stop codons along the way'.  'to_first_stop' is
> > clearer, to my mind, and even that leaves out the potential (and
> > hopefully redundant) qualifier 'in-frame' ;)
> > 
> 
> I agree with Leighton here, "to_end" sounds like "to the end of the sequence
> given".  I quite like "to_first_stop", but it is longer than "to_stop".
> 

Either is fine with me.


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