[Biopython-dev] New Biopython release coming up / Alphabets

Peter biopython-dev at maubp.freeserve.co.uk
Thu Jul 6 09:06:07 UTC 2006

Peter wrote:
>> Bugzilla Bug 1987 Alphabet.Gapped does not retain gap character
>> http://bugzilla.open-bio.org/show_bug.cgi?id=1987
>> I have attached a suggested patch, second opinion welcome

Michiel de Hoon wrote:
> Whereas the patch looks fine, I have no idea what this code is supposed 
> to do, or why it needs to be so complicated.

I'm not the person to ask.

The whole Alphabet is something that confused me a little when first 
using BioPython.  I see why a special class for sequences is a nice 
idea, and that handling the different variants of RNA, DNA and proteins 
is a good idea.

But to be honest, I have generally used plain strings in my own 
programs, and meddled with alphabets only when needed (e.g. for 
translating from DNA to protein sequences).


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