[Biopython-dev] Reduced alphabets

Iddo Friedberg idoerg at burnham.org
Wed Mar 17 20:52:08 EST 2004

Hi Brad,

Document my code? Why do you think they call it "code"?

OK, I'll do it. Tomorrow. After I recover from the green beer we are 
about to consume as part of a farewell party+St. Patrick's day lab night 
on the town....


Brad Chapman wrote:
> 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
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Iddo Friedberg, Ph.D.
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 713 9930

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