[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 #42 from biopython-bugzilla at maubp.freeserve.co.uk  2008-11-06 09:46 EST -------
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".


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