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

[Michiel Jan Laurens de Hoon]

Marc Colosimo wrote:
>> [Michiel]
>> It appears that most people (myself included) use plain strings instead
>> of Seq objects (= string + Alphabet). We should check on the biopython
>> mailing list if anybody really needs alphabets, and if not get rid of
>> them (after the upcoming Brooklyn-release (1.42) though).
 >
 > [Marc]
> I am strongly arguing  against removing the alphabets. You would loss 
> all of the cool features of Seq Objects (complement, 
> reverse_complement).  There are similar functions under Bio.SeqUtils but 
> those are "Deprecated". From just looking around, I think this would 
> break many things.

There is a function reverse_complement in Bio.Seq that works on plain 
strings. (If you need the complement instead, you can of course reverse 
the result). So can you be more specific on which features of Seq 
objects are actually needed? While I can see the intuitive appeal of 
having a Seq class, I cannot think of any practical cases where a simple 
string wouldn't do.

--Michiel.


-- 
Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032