[Biopython-dev] [Bug 2530] Bio.Seq.translate() treats invalid codons as stops

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sun Jun 29 14:35:11 UTC 2008


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
 Attachment #954 is|0                           |1
           obsolete|                            |

------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk  2008-06-29 10:35 EST -------
Created an attachment (id=955)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=955&action=view)
Patches Bio/Data/CodonTable.py for ambiguous start/stop codons

This implements the stub function list_ambiguous_codons, and adds a lot of
in-situ asserts which could later be moved to a unit test.

e.g. ['TAG', 'TAA'] -> ['TAG', 'TAA', 'TAR']
     ['UAG', 'UGA'] -> ['UAG', 'UGA', 'URA']

Note that ['TAG', 'TGA'] -> ['TAG', 'TGA'], this does not add 'TRR' is this
could be a stop codon or a coding amino acid.  Thus only two more codons are
added in the following example:

e.g. ['TGA', 'TAA', 'TAG'] -> ['TGA', 'TAA', 'TAG', 'TRA', 'TAR']

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