[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


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

           What    |Removed                     |Added
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 Attachment #795 is|0                           |1
           obsolete|                            |




------- Comment #11 from biopython-bugzilla at maubp.freeserve.co.uk  2007-12-15 08:47 EST -------
Created an attachment (id=836)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=836&action=view)
Patch to Bio/Seq.py

[Note this does not update the test suite or the documentation, which would be
needed if this is committed]

Adds new methods to the MutableSeq object:
- transcribe (in place)
- back_transcribe (in place)

Adds new methods to the Seq object:
- transcribe
- back_transcribe
- translate (like the python string method)
- translate_all (Biological translation)
- translate_to_stop (Biological translation up to and excluding first stop
codon)
- translate_cds (Biological translation with an initial start codon as M, up to
and excluding the first stop codon)

I think this would be enough to deprecate Bio.Translate and Bio.Transcribe
(after the next release).

Comments welcome - for example are these method names sensible?

Also, should the MutableSeq methods all act "in situ"?  What about translation
methods for MutableSeq objects?


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