def test_popcnt():
x = 466311136197825
y = x
c = 0
while y > 0:
c += y & 1
y >>= 1
j = bits.popcnt(x)
assert c == j
def ham(x, y):
"""
Compute the Hamming distance between two k-mers `x` and `y`.
Although *k* is not a parameter, *k*-mers longer than 30bp are not
guaranteed to produce correct results.
"""
z = x ^ y
# NB: if k > 32, the constant below will need extending.
v = (z | (z >> 1)) & m1
return popcnt(v)
def grp(itms):
z = len(itms)
u = unionfind()
for i in xrange(z):
for j in xrange(i + 1, z):
d0 = lev(K, itms[i], itms[j])
if d0 <= d:
u.union(i, j)
idx = {}
for i in xrange(z):
j = u.find(i)
if j not in idx:
idx[j] = []
idx[j].append(i)
for ys in idx.itervalues():
if len(ys) == 1:
continue
zs = [itms[y] for y in ys]
m = 0
for z in zs:
m |= 1 << ((z >> T) & 3)
if popcnt(m) == 1:
continue
yield zs
def ham(x, y):
"Compute the hamming distance between two k-mers."
z = x ^ y
# NB: if k > 32, the constant below will need extending.
v = (z | (z >> 1)) & m1
return popcnt(v)