def test_all_huddinge_pairs_shuffle(kmers):
import pyhuddinge as ph
D1 = ph.all_pairs_huddinge_distance(kmers)
D2 = ph.all_pairs_huddinge_distance(kmers[::-1])
Dsq1 = ph.squareform(D1, kmers)
Dsq2 = ph.squareform(D2, kmers[::-1])
reordered2 = Dsq2[Dsq1.columns].loc[Dsq1.index]
#print(Dsq1)
#print(reordered2)
assert (Dsq1 == reordered2).all().all()
def test_all_huddinge_pairs1():
import pyhuddinge as ph
kmers = ["AAGGGAA", "AAAGCAA", "AAACCAA", "AAACAAA"]
import itertools as it
kmers = ["".join(x) for x in it.product("ACGT", repeat=6)]
D = ph.all_pairs_huddinge_distance(kmers)
assert len(D) == len(kmers) * (len(kmers) - 1) / 2
assert min(D) > 0
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_all_huddinge_pairs_puregap():
import pyhuddinge as ph
kmers = ['nnnnnnnnnnnn', 'nnn']
with pytest.raises(ValueError):
D1 = ph.all_pairs_huddinge_distance(kmers)
def test_all_huddinge_pairs_empty():
import pyhuddinge as ph
kmers = []
with pytest.raises(ValueError):
D1 = ph.all_pairs_huddinge_distance(kmers)
def test_all_huddinge_pairs_nonbase(kmers):
import pyhuddinge as ph
with pytest.raises(ValueError):
D1 = ph.all_pairs_huddinge_distance(kmers)