[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 #7 from biopython-bugzilla at maubp.freeserve.co.uk  2007-10-18 06:35 EST -------
Michiel in comment 6 wrote:
> If we add translate, transcribe methods to Seq objects, can we then
> deprecate Bio.Transcribe, Bio.Translate?

Bio.Transcribe - Yes
====================
Bio.Transcribe is so trivial we could recreate that code in Bio.Seq and then
deprecate Bio.Transcribe without losing any functionality:
- transcibe
- back_transcibe

Bio.Translate - Maybe
=====================
Initially I was just proposing to add:
- translate (including all stop codons)

I was simply going to have Bio.Seq call Bio.Translate to do the work.

It would be nice to simplify Biopython by also deprecating Bio.Translate, but
if we want to do this without loss of current functionality we need to consider
including the following in Bio.Seq:
- translate_to_stop (all amino acids up to but excluding the first stop)
- back_translate (gives a single possible nucleotide sequence)


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