[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 #23 from lpritc at scri.sari.ac.uk  2008-10-20 05:48 EST -------
(In reply to comment #22)

> (a) Validate the first codon is a valid start codon, and translate it as M
> (even if going on the genetic code it would normally be say L).  This should be
> a boolean argument defaulting to False, possible names "start", "check_start",
> "from_start", ...

> (b) 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).
> 
> You might want to control these two options independently, so having them as
> two arguments is more flexible.

Further to the above (and keeping away from ORF-finding) another use-case would
be translation of ESTs, which may come with or without either a start or a stop
codon.  Often I am handed compilations of EST sets that have been obtained
using different experimental methods, and are not consistently 3` or 5`
sequenced (nor, to be fair, are they uniformly in the correct orientation...),
and in those cases I would wish to translate the entire sequence without regard
to the presence of a start or stop codon (really I'd like to find ORFs, but I
promised I'd keep away from that, for now ;) ).

I would prefer that default behaviour did not enforce either a start or stop
codon check, but that each of these could be optional arguments. 


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