def test_to_pssm_pseudocount(self):
"""produces a PSSM array with pseudocount"""
data = array([
[10, 30, 50, 10],
[25, 25, 25, 25],
[5, 80, 0, 10],
[70, 10, 10, 10],
[60, 15, 0, 20],
])
marr = MotifCountsArray(array(data), "ACGT")
adj = data + 1
got = marr.to_pssm(pseudocount=1)
freqs = marr._to_freqs(pseudocount=1)
expect = log2(freqs / 0.25)
assert_allclose(got.array, expect, atol=1e-3)
def test_to_pssm(self):
"""produces a PSSM array"""
data = array([
[10, 30, 50, 10],
[25, 25, 25, 25],
[5, 80, 5, 10],
[70, 10, 10, 10],
[60, 15, 5, 20],
])
marr = MotifCountsArray(array(data), "ACGT")
got = marr.to_pssm()
expect = array([
[-1.322, 0.263, 1.0, -1.322],
[0.0, 0.0, 0.0, 0.0],
[-2.322, 1.678, -2.322, -1.322],
[1.485, -1.322, -1.322, -1.322],
[1.263, -0.737, -2.322, -0.322],
])
assert_allclose(got.array, expect, atol=1e-3)