Vince's version of entropy in Python

entropy_vince.py

"""
entropy.py

Calculate entropy of a given list.
"""
from math import log, log10
from collections import Counter
import pdb

def entropy(x, logfun=lambda x: log(x, 2)):
    """Calculate the entropy for a list of objects `x`, using the log
    function `logfun`.
    """
    counts = Counter()
    total = 0.0
    for item in x:
        total += 1
        counts[item] += 1
    probs = [counts[k]/total for k in counts]
    ent = -sum([p*logfun(p) for p in probs])
    return ent

if __name__ == "__main__":
    seq_1 = "GA GA GA GA GT GA GA GA GA GT CG CG GA GA".split()
    seq_2 = "GA CG TG AG GC AG GT GC AT TA CC AA TT GG".split()

    # simple unit tests
    EPS = 1e-6
    assert(entropy(seq_1) - 1.97638209746 < EPS) 
    assert(entropy(seq_2) - 3.52164063634 < EPS)