Loop from 'aaaa' to 'tttt' ?

Des Small des.small at bristol.ac.uk
Mon Jun 16 19:42:40 CEST 2003


Lars Schaps <tuffi23 at gmx.de> writes:

> Hello.
> 
> In my program in need a loop from 'aaaa' over
> 'aaac', 'aaag', 'aaat', 'aaca' to 'tttt'.
> (Possible characters 'a', 'c', 'g' and 't')
> 
> One idea i had is to take a number n with the base of
> 4 and use 
> 
> t= string.translate( '0123', 'acgt')
> string.translate( n, t)
> 
> But i don't know how to convert from base10 to base4.
> 
> Has anyone a idea?


I like to use recursive generators for this sort of thing:

from __future__ import generators # Not needed in python 2.3

def base_iter():
    for a in 'acgt': yield a

def nbase_iter(n):
    if n==0: yield '' 
    else:
        for first in base_iter():
            for rest in nbase_iter(n-1):
                yield first + rest

After which you can do:

>>> list(nbase_iter(4))[:5]
['aaaa', 'aaac', 'aaag', 'aaat', 'aaca']
>>> list(nbase_iter(4))[-5:]
['ttgt', 'ttta', 'tttc', 'tttg', 'tttt']

Des
always wanted to do some bioinformatics.
-- 
Des Small / Scientific Programmer/ School of Mathematics /
University of Bristol / UK / Word falling / Image falling




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