[BioPython] Translation method for Seq object

Peter biopython at maubp.freeserve.co.uk
Tue Oct 14 10:18:13 UTC 2008


OK, we seem to have a consensus :)

In Biopython's CVS, the Seq object now has a translate method which
does a biological translation.  If anyone comes up with a better
proposal before the next release, we can still rename this.  Otherwise
I will update the Tutorial in CVS shortly...

Note that for now, I have followed the existing Bio.Seq.translate(...)
function and the new Seq object translate(...) method takes only two
optional parameters - the codon table and the stop symbol.  I have
noted some suggestions for possible additional arguments on Bug 2381.

The adventurous among you may want to use CVS to update your Biopython
installations to try this out.  Please note that you will now need
numpy instead of Numeric (there is nothing to stop you having both
numpy and Numeric installed at the same time).  If you do try out the
CVS code, please run the unit tests and report any issues.

Thanks,

Peter



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