import numpy as np
import scipy as sp

from Bio import Restriction as rst
from Bio.Seq import Seq
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA

bases = [['A','T'],['C','G']]

def get_genome(size, gc):
    i = 0
    genome = ""
    while i < size:
        r = np.random.randint(0,100)
        b = bases[0]
        if r < gc:
            b = bases[1]
        genome += b[np.random.random_integers(0,1)]
        i += 1
    return genome

def get_gc(g):
    gc = 0
    for x in genome:
        if x == "G" or x == "C":
            gc += 1.0
    return gc/len(genome)

genome = get_genome(1e6,60)
get_gc(genome)

amb = IUPACAmbiguousDNA()

g = Seq(genome, amb)

rb = rst.EcoRI + rst.MstI

rb

ana = rst.Analysis(rb, g, linear=True)

ana.with_sites()

import Bio
print Bio.__version__

import IPython
print IPython.__version__

import sys
print sys.version