def test_to_freqs_pseudocount(self):
"""produces a freqs array with pseudocount"""
data = array([[2, 4], [3, 5], [0, 8]])
marr = MotifCountsArray(array(data), "AB")
got = marr.to_freq_array(pseudocount=1)
adj = data + 1
expect = adj / vstack(adj.sum(axis=1))
assert_allclose(got.array, expect)
got = marr.to_freq_array(pseudocount=0.5)
adj = data + 0.5
expect = adj / vstack(adj.sum(axis=1))
assert_allclose(got.array, expect)
def test_to_freqs_1d(self):
"""produce a freqs array from 1D counts"""
data = [43, 48, 114, 95]
total = sum(data)
a = MotifCountsArray([43, 48, 114, 95], motifs=("T", "C", "A", "G"))
f = a.to_freq_array()
assert_allclose(f.array, array([v / total for v in data], dtype=float))
def test_to_freqs(self):
"""produces a freqs array"""
data = array([[2, 4], [3, 5], [4, 8]])
marr = MotifCountsArray(array(data), "AB")
expect = data / vstack(data.sum(axis=1))
got = marr.to_freq_array()
assert_allclose(got.array, expect)
def test_slicing(self):
"""slice by keys should work"""
counts = MotifCountsArray(
[[3, 2, 3, 2], [3, 2, 3, 2]],
["A", "C", "G", "T"],
row_indices=["DogFaced", "FlyingFox"],
)
freqs = counts.to_freq_array()
got = freqs["FlyingFox"].to_array()
assert_allclose(got, [0.3, 0.2, 0.3, 0.2])