def hamming_distance(seq_1, seq_2, ignore_case):
"""Hamming distance between two sequences
Calculate the Hamming distance between SEQ_1 and SEQ_2.
"""
result = pb.hamming_distance(seq_1, seq_2, ignore_case=ignore_case)
click.echo(result)
def test_hamming_distance_ignore_case():
expect = 0
result = pb.hamming_distance("CAGATA", "cagata", ignore_case=True)
assert result == expect
def test_hamming_distance_different_case():
expect = 6
result = pb.hamming_distance("CAGATA", "cagata", ignore_case=False)
assert result == expect
def test_hamming_distance_error():
with pytest.raises(ValueError):
pb.hamming_distance("CAGATA", "CACACACA")
def test_hamming_distance_many():
expect = 6
result = pb.hamming_distance("CAGATA", "GTCTAT")
assert result == expect
def test_mutate_sequence_aa_many(sample_aa_sequence):
result = pb.mutate_sequence(sample_aa_sequence, mutations=10,
alphabet="aa")
assert len(result) == len(sample_aa_sequence)
assert set(result) == set(pb._AA_LIST)
assert pb.hamming_distance(sample_aa_sequence, result) <= 10
def test_mutate_sequence_nt_many(sample_nt_sequence):
result = pb.mutate_sequence(sample_nt_sequence, mutations=10)
assert len(result) == len(sample_nt_sequence)
assert set(result) == set(pb._NT_LIST)
assert pb.hamming_distance(sample_nt_sequence, result) <= 10
def test_hamming_distance_one():
expect = 1
result = pb.hamming_distance("CAGATA", "CACATA")
assert result == expect
def test_hamming_distance_zero():
expect = 0
result = pb.hamming_distance("CAGATA", "CAGATA")
assert result == expect