[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 #3 from biopython-bugzilla at maubp.freeserve.co.uk  2007-10-16 06:46 EST -------
Doing a three/six frame translation is however fairly common, and perhaps
warrents an "official" implementation in Bio.SeqUtils

My current inclination is try and keep the Bio.Seq translation function as
simple as possible.  There are lots of possible options to worry about...
catering to them all could make the translate method rather daunting.

Perhaps things like the frame (or even the starting nucleotide) could be done
in Bio.Translate only.  Another "special case" example I personally would like
is an option to check the first codon is a valid start codon for the specified
codon table, and to translate it as methionine (M).  Then there is the question
of if Bio.Translate's "translate_to_stop" functionality should be exposed in a
Seq method.

Note there is yet another (!) translation function Bio.SeqUtils.translate()
which is frame aware [personally I would mark a lot of this module as
deprecated].


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