def test_score_str(self):
"""produce correct score from seq"""
data = [
[0.1, 0.3, 0.5, 0.1],
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.8, 0.05, 0.1],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
pssm = PSSM(data, "ACTG")
seq = "".join("ACTG"[i] for i in [3, 1, 2, 0, 2, 2, 3])
scores = pssm.score_seq(seq)
assert_allclose(scores, [-4.481, -5.703, -2.966], atol=1e-3)
with self.assertRaises(ValueError):
pssm.score_seq(seq[:3])
def test_score_seq_obj(self):
"""produce correct score from seq"""
from cogent3 import DNA
data = [
[0.1, 0.3, 0.5, 0.1],
[0.25, 0.25, 0.25, 0.25],
[0.05, 0.8, 0.05, 0.1],
[0.7, 0.1, 0.1, 0.1],
[0.6, 0.15, 0.05, 0.2],
]
pssm = PSSM(data, "ACTG")
seq = DNA.make_seq("".join("ACTG"[i] for i in [3, 1, 2, 0, 2, 2, 3]))
scores = pssm.score_seq(seq)
assert_allclose(scores, [-4.481, -5.703, -2.966], atol=1e-3)
