[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 #24 from biopython-bugzilla at maubp.freeserve.co.uk  2008-10-28 11:25 EST -------
(In reply to comment #22)
> ... Stop translating at the first in frame stop codon (see my comment 18). 
> Again, a boolean argument, and for compatibility with previous Biopython
> conventions, defaulting to False (i.e. read through).  Possible names "stop",
> "to_stop", "auto_stop", "terminate", ...
> 
> In this case, how should the method behave if there is no final stop codon -
> raise an error or not?  Also should the stop codon be included in the returned
> sequence (note that the Bio.Translate module did not include the stop symbol).

Added in CVS with the optional argument named "to_stop" (boolean), defaulting
to False (continue translating through any stops).

See Bio/Seq.py revision 1.51 and Tests/test_seq.py revision 1.28

I'm happy to discuss alternative names for this argument (up until the next
release of Biopython).  This choice was influenced by the existing method name
translate_to_stop in Bio.Translate (which can now be declared obsolete and
awaiting deprecation).


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