[Biopython-dev] [Bug 2381] translate and transcibe methods for the Seq object (in Bio.Seq)

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2381





------- Comment #14 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-21 11:38 EST -------
For comparison, the following is copied from the BioPerl documentation about
their sequence object's translate method.  It would be nice to follow some of
the same naming conventions for any optional arguments.

http://www.bioperl.org/Core/Latest/bptutorial.html#iii_3_1_manipulating_sequence_data_with_seq_methods

If we want to translate full coding regions (CDS) the way major nucleotide
databanks EMBL, GenBank and DDBJ do it, the translate() method has to perform
more checks. Specifically, translate() needs to confirm that the sequence has
appropriate start and terminator codons at the very beginning and the very end
of the sequence and that there are no terminator codons present within the
sequence in frame 0. In addition, if the genetic code being used has an
atypical (non-ATG) start codon, the translate() method needs to convert the
initial amino acid to methionine. These checks and conversions are triggered by
setting ``complete'' to 1:

  $prot_obj = $my_seq_object->translate(-complete => 1);


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