def test_huddinge_upperlower(x, y):
import pyhuddinge as ph
h_dist_ll = ph.huddinge_distance(x, y)
h_dist_lu = ph.huddinge_distance(x, y.upper())
h_dist_uu = ph.huddinge_distance(x.upper(), y.upper())
h_dist_ul = ph.huddinge_distance(x.upper(), y)
assert h_dist_ll == h_dist_lu
assert h_dist_ll == h_dist_ul
assert h_dist_ll == h_dist_uu
def test_huddingepair_rc_closer(x, y):
import pyhuddinge as ph
h_dist = ph.huddinge_distance(x, y, False)
h_dist_rc = ph.huddinge_distance(y, x, True)
assert (h_dist >= h_dist_rc)
if min(len(x.strip("n")), len(y.strip("n"))) > 0:
assert (h_dist == 0 and x.strip("n") == y.strip("n")) or h_dist > 0
assert h_dist <= max(len(x.strip("n")), len(y.strip("n"))), h_dist
def test_huddingepair_rev_comp(x, y):
import pyhuddinge as ph
h_dist = ph.huddinge_distance(x, y)
h_dist_rc = ph.huddinge_distance(x, y, True)
h_dist_rcx = ph.huddinge_distance(reverse_complement(x), y)
h_dist_rcy = ph.huddinge_distance(x, reverse_complement(y))
h_dist_rcxy = ph.huddinge_distance(reverse_complement(x),
reverse_complement(y))
assert h_dist == h_dist_rcxy
assert h_dist_rc <= h_dist
assert h_dist_rc == min(h_dist_rcx, h_dist)
assert h_dist_rcx == h_dist_rcy
def test_ungapkmers_PMC4362205_figS1B_ACnGT():
import pyhuddinge as ph
A = "ACGT"
ex = {"ACCT": 1, "CGTT": 1}
for B, d in ex.items():
print(A, B)
assert ph.huddinge_distance(A, B) == d, (A, B, d)
def test_huddingepair1():
import pyhuddinge as ph
x, y = "AAAAAAA", "AAATAAA"
h_dist = ph.huddinge_distance(x, y)
assert h_dist == 1
def test_huddingepair_symmetry(x, y, reverse_complements):
import pyhuddinge as ph
h_dist = ph.huddinge_distance(x, y, reverse_complements)
if reverse_complements:
assert (h_dist == 0 and
(x.strip("n") == y.strip("n")
or x.strip("n") == reverse_complement(y).strip("n"))
or min(len(x.strip("n")), len(y.strip("n")))
== 0) or (h_dist > 0 and x != y and x != reverse_complement(y))
else:
assert (h_dist == 0 and x.strip("n") == y.strip("n")
or min(len(x.strip("n")), len(y.strip("n")))
== 0) or (h_dist > 0 and x.strip("n") != y.strip("n"))
assert h_dist <= max(len(x), len(y)), h_dist
h_dist_v = ph.huddinge_distance(y, x, reverse_complements)
assert h_dist_v == h_dist
def test_all_huddinge_pairs_concordance(kmers, reverse_complements):
import pyhuddinge as ph
print(repr(kmers), file=open("dump.py", "w"))
D = ph.all_pairs_huddinge_distance(kmers, reverse_complements)
assert len(D) == len(kmers) * (len(kmers) - 1) / 2
Dsq = ph.squareform(D, kmers)
for i in Dsq.index:
for j in Dsq.columns:
if i < j:
assert Dsq.loc[i, j] == ph.huddinge_distance(
i, j, reverse_complements)
def test_huddingepair_nonbase(x, y):
import pyhuddinge as ph
with pytest.raises(ValueError):
h_dist = ph.huddinge_distance(x, y)