[Biopython-dev] Reduced alphabets

[Brad Chapman]

Hi Iddo;

> Thanks to overwhelming demand (well, nobody really objected ;) biopython
> now has the rudimentaries for handling reduced alphabets. I committed
> the following changes:
> 
> 1) in Bio.utils I added
> 
>   reduce_sequence(seq, reduction_table, new_alphabet=None)
> 
> 2) in Alphabet, I added Reduce.py, which has reduction tables, and
> reduced alphabet definitions + literature citations

Thanks for this. Sorry I didn't have a chance to weigh in earlier,
but I was out of town (actually on Biopython business). 

Everything looks good -- my only suggestion would be to add a bit
more documentation to the modules, specifically Alphabet/Reduced.py.
I think just copying and pasting the relevant bits from your
original e-mail to a doc-string at the top would be a real help for
someone searching around and saying "wellllll...what do we have
here."

Other than that, all good. Thanks for the fix on count_monomers -- I
do think that's the right thing to do. We should really discourage
using MutableSeqs (which is where the array stuff comes from) on
for anything besides, well, mutating them -- so this fix is fine.

Thanks for the contribution!
Brad