def test_jsm(self):
"""evaluate jsm between identical, and non-identical distributions"""
case1 = [
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.0],
]
for index in range(len(case1[0])):
case1[0][index] = 1.0
case1[1][index] = 1.0
assert_allclose(
jsm(case1[0], case1[1], validate=True),
0.0,
err_msg="Testing case1 for jsm failed",
atol=self.atol,
)
case1[0][index] = 0.0
case1[1][index] = 0.0
# case2 is testing the numerical output of jsm between two random distributions
case2 = [[1 / 10, 9 / 10, 0], [0, 1 / 10, 9 / 10]]
assert_allclose(
jsm(case2[0], case2[1], validate=True),
0.8749298275892526,
err_msg="Testing case2 for jsm failed",
atol=self.atol,
)
# case3 is testing the numerical output of jsm between two random distributions
case3 = [[1.0, 0.0], [1 / 2, 1 / 2]]
assert_allclose(
jsm(case3[0], case3[1], validate=True),
0.5579230452841438,
err_msg="Testing case3 for jsm failed",
atol=self.atol,
)
# case4 is testing if the jsm between two identical uniform distributions is 0.0
case4 = [
[1 / 10] * 10,
[1 / 10] * 10,
]
assert_allclose(
jsm(case4[0], case4[1], validate=True),
0.0,
err_msg="Testing case4 for jsm failed",
atol=self.atol,
)
def test_jsm(self):
"""case1 is testing if the jsm between two identical distributions is 0.0"""
case1 = [
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
]
for pointer in range(10):
case1[0][pointer] = 1.0
case1[1][pointer] = 1.0
assert_allclose(
jsm(case1[0], case1[1], validate=True),
0.0,
err_msg="Testing case1 for jsm failed",
)
case1[0][pointer] = 0.0
case1[1][pointer] = 0.0
"""case2 is testing the numerical output of jsm between two random distributions"""
case2 = [[1.0 / 10, 9.0 / 10, 0], [0, 1.0 / 10, 9.0 / 10]]
assert_allclose(
jsm(case2[0], case2[1], validate=True),
0.8749298275892526,
err_msg="Testing case2 for jsm failed",
)
"""case3 is testing the numerical output of jsm between two random distributions"""
case3 = [[1.0, 0.0], [0.5, 0.5]]
assert_allclose(
jsm(case3[0], case3[1], validate=True),
0.5579230452841438,
err_msg="Testing case3 for jsm failed",
)
"""case4 is testing if the jsm between two identical uniform distributions is 0.0"""
case4 = [
[0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1],
[0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1],
]
assert_allclose(
jsm(case4[0], case4[1], validate=True),
0.0,
err_msg="Testing case4 for jsm failed",
)
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)