def test_phred_conversions():
assert util.phred_to_prob(40) == 0.9999
assert util.phred_to_prob(30) == 0.999
assert util.phred_to_prob(20) == 0.99
assert util.phred_to_prob(10) == 0.9
assert util.prob_to_phred(0.9999) == 40
assert util.prob_to_phred(0.999) == 30
assert util.prob_to_phred(0.99) == 20
assert util.prob_to_phred(0.9) == 10
def gen_phred_scores(self, mean_quality, orientation):
"""Generate a normal distribution, transform to phred scores
Generate a list of phred score according to a normal distribution
centered around the ErrorModel quality
Args:
mean_quality (int): mean phred score
Returns:
list: list of phred scores following a normal distribution
"""
norm = [min(q, 0.9999) for q in np.random.normal(
util.phred_to_prob(mean_quality), 0.01, self.read_length)]
phred = [util.prob_to_phred(p) for p in norm]
return phred