def test_pairwise_(self):
"""returns None when single row"""
# ndim=1
data = [0.25, 0.25, 0.25, 0.25]
freqs = MotifFreqsArray(array(data), "ACGT")
got = freqs.pairwise_jsm()
self.assertEqual(got, None)
# ndim=2
data = array([[0.25, 0.25, 0.25, 0.25]])
freqs = MotifFreqsArray(data, "ACGT")
got = freqs.pairwise_jsm()
self.assertEqual(got, None)
def test_pairwise_jsm(self):
"""correctly constructs pairwise JS metric dict"""
from numpy.random import random
from cogent3.maths.measure import jsm
data = [[0.25, 0.25, 0.25, 0.25], [0.5, 0.5, 0, 0]]
expect = jsm(data[0], data[1])
freqs = MotifFreqsArray(array(data), "ACGT")
got = freqs.pairwise_jsm()
assert_allclose(list(got.values())[0], expect)
data = []
for _ in range(6):
freqs = random(4)
freqs = freqs / freqs.sum()
data.append(freqs)
freqs = MotifFreqsArray(array(data), "ACGT")
pwise = freqs.pairwise_jsm()
self.assertEqual(len(pwise), 6 * 6 - 6)