def test_lev():
s0 = "CAAAAAAAAAAAAAAAATTTTTTTT"
s1 = "CAAAAAAAAAAAAATTTTTTTTCGG"
k = len(s0)
x0 = basics.kmer(s0)
x1 = basics.kmer(s1)
assert basics.lev(k, x0, x1) == 3
def test_ham():
random.seed(17)
k = 25
a = ''.join([random.choice("ACGT") for i in range(k)])
b = ''.join([random.choice("ACGT") for i in range(k)])
x = basics.kmer(a)
y = basics.kmer(b)
h = 0
for i in range(k):
if a[i] != b[i]:
h += 1
j = basics.ham(x, y)
assert h == j
def test_kmers():
s = "CCTCGTACGCCATATTTTCGCATTTCACGTACGTATTGTTTTTGCAACATAATTACCTATTCTCTTTTGGGGGGGGTTTTAGGCATTCCATTTAATNGCTTTTCTTTTAATGCATGGAGTTTTTCCCATTCATCCTTTGATATATTATCTTTACTTGCTTCGAAGTCTNTTGCTGTGAGATGTATATCTTCTGGATGGATTTGTTTACGTTCTTTTGTTACTGGATCTATAGTAAATGGAATCATTTCCTT"
k = 25
xs = list(basics.kmers(k, s, False))
ys = []
for i in range(len(s) - k + 1):
y = basics.kmer(s[i:i + k])
if y is not None:
ys.append(y)
assert xs == ys
def test_lcp():
random.seed(17)
k = 25
a = ''.join([random.choice("ACGT") for i in range(k)])
x = basics.kmer(a)
y = x ^ (1 << 18)
b = basics.render(k, y)
h = 0
for i in range(k):
h = i
if a[i] != b[i]:
break
j = basics.lcp(k, x, y)
assert h == j
def test_rc_1():
s = "CTTTTTTT"
k = len(s)
x = basics.kmer(s)
y = basics.rc(k, x)
assert y == 2
def test_kmer_CpolyA():
s = "CAAAAAAAAAAAAAAAAAAAAAAAA"
x = basics.kmer(s)
assert x == (1 << 48)
def test_kmer_polyAT():
s = "AAAAAAAAAAAAAAAAAAAAAAAAT"
x = basics.kmer(s)
assert x == 3
def test_kmer_polyAG():
s = "AAAAAAAAAAAAAAAAAAAAAAAAG"
x = basics.kmer(s)
assert x == 2
def test_kmer_polyAC():
s = "AAAAAAAAAAAAAAAAAAAAAAAAC"
x = basics.kmer(s)
assert x == 1
def test_kmer_polyA():
s = "AAAAAAAAAAAAAAAAAAAAAAAAA"
x = basics.kmer(s)
assert x == 0
def probe(s):
return (len(s), kmer(s))