def test_add(self):
s = HyperLogLog(0.05)
for i in range(10):
s.add(str(i))
M = [(i, v) for i, v in enumerate(s.M) if v > 0]
self.assertEqual(M, [(1, 1), (41, 1), (44, 1), (76, 3), (103, 4), (182, 1), (442, 2), (464, 5), (497, 1), (506, 1)])
def test_pickle(self):
a = HyperLogLog(0.05)
for x in range(100):
a.add(str(x))
b = pickle.loads(pickle.dumps(a))
self.assertEqual(a.M, b.M)
self.assertEqual(a.alpha, b.alpha)
self.assertEqual(a.p, b.p)
self.assertEqual(a.m, b.m)
def test_pickle(self):
a = HyperLogLog(0.05)
for x in range(100):
a.add(str(x))
b = pickle.loads(pickle.dumps(a))
self.assertEqual(a.M, b.M)
self.assertEqual(a.alpha, b.alpha)
self.assertEqual(a.p, b.p)
self.assertEqual(a.m, b.m)
def test_add(self):
s = HyperLogLog(0.05)
for i in range(10):
s.add(str(i))
M = [(i, v) for i, v in enumerate(s.M) if v > 0]
self.assertEqual(M, [(1, 1), (41, 1), (44, 1), (76, 3), (103, 4),
(182, 1), (442, 2), (464, 5), (497, 1), (506, 1)])
def test_calc_cardinality(self):
clist = [1, 5, 10, 30, 60, 200, 1000, 10000, 60000]
n = 30
rel_err = 0.05
for card in clist:
s = 0.0
for c in xrange(n):
a = HyperLogLog(rel_err)
for i in xrange(card):
a.add(os.urandom(20))
s += a.card()
z = (float(s) / n - card) / (rel_err * card / math.sqrt(n))
self.assertLess(-1.96, z)
self.assertGreater(1.96, z)
def test_calc_cardinality(self):
clist = [1, 5, 10, 30, 60, 200, 1000, 10000, 60000]
n = 30
rel_err = 0.05
for card in clist:
s = 0.0
for c in range(n):
a = HyperLogLog(rel_err)
for i in range(card):
a.add(os.urandom(20))
s += a.card()
z = (float(s) / n - card) / (rel_err * card / math.sqrt(n))
self.assertLess(-3, z)
self.assertGreater(3, z)
def test_save(self):
a = HyperLogLog(0.05)
for x in range(100):
a.add(str(x))
saved=a.save()
b = HyperLogLog(0.05)
b.load(saved)
self.assertEqual(a.M, b.M)
self.assertEqual(a.alpha, b.alpha)
self.assertEqual(a.p, b.p)
self.assertEqual(a.m, b.m)
def test_update(self):
a = HyperLogLog(0.05)
b = HyperLogLog(0.05)
c = HyperLogLog(0.05)
for i in xrange(2):
a.add(str(i))
c.add(str(i))
for i in xrange(2, 4):
b.add(str(i))
c.add(str(i))
a.update(b)
self.assertNotEqual(a, b)
self.assertNotEqual(b, c)
self.assertEqual(a, c)
def test_update(self):
a = HyperLogLog(0.05)
b = HyperLogLog(0.05)
c = HyperLogLog(0.05)
for i in range(2):
a.add(str(i))
c.add(str(i))
for i in range(2, 4):
b.add(str(i))
c.add(str(i))
a.update(b)
self.assertNotEqual(a, b)
self.assertNotEqual(b, c)
self.assertEqual(a, c)
def test_init(self):
s = HyperLogLog(0.05)
self.assertEqual(s.p, 9)
self.assertEqual(s.alpha, 0.7197831133217303)
self.assertEqual(s.m, 512)
self.assertEqual(len(s.M), 512)
def test_update_err(self):
a = HyperLogLog(0.05)
b = HyperLogLog(0.01)
self.assertRaises(ValueError, a.update, b)
import khmer
import sys
from screed.fasta import fasta_iter
from hyperloglog.hll import HyperLogLog
filename = sys.argv[1]
K = int(sys.argv[2]) # size of kmer
ERROR_RATE = .01
TT = string.maketrans('ACGT', 'TGCA')
hllcpp = khmer.new_hll_counter(ERROR_RATE)
hlllib = HyperLogLog(ERROR_RATE)
counter = Counter()
counter_norc = Counter()
for n, record in enumerate(fasta_iter(open(filename))):
sequence = record['sequence']
seq_len = len(sequence)
for n in range(0, seq_len + 1 - K):
kmer = sequence[n:n + K]
rc = kmer[::-1].translate(TT)
hllcpp.add(kmer)
hlllib.add(kmer)
counter_norc.update([kmer])
if rc in counter:
