test_simulate_seq.py 文件源码

def test_simulate_sequencing_errors(self):
        """Test function simulating sequencing errors."""
        error_rate = 0.1
        error_weights = {'substitution': 1.0 / 6,
                         'insertion': 1.0 / 6,
                         'deletion': 4.0 / 6}
        sequence = sim_seq.simulate_sequence(5000)
        mutated_record = sim_seq.simulate_sequencing_errors(
            sequence, error_rate, error_weights)
        distance = editdistance.eval(sequence, mutated_record.seq)
        expected_errors = len(sequence) * error_rate
        errors_sd = np.sqrt(len(sequence) * error_rate * (1 - error_rate))
        # Should pass 0.9973 proportion of cases:
        self.assertTrue(expected_errors - errors_sd * 3 < distance < expected_errors +
                        errors_sd * 3, msg="expected: {} realised:{}".format(expected_errors, distance))