def test_single_cpg(self, algorithm):
seq_str = 'CG'
computed = algorithm(make_seq_record(seq_str), 2, 1, 2)
expected = make_algo_results(seq_str, [(0, 2, 1, 2)])
print computed.seq_record.features[0].extract(computed.seq_record.seq)
for a in [computed, expected]:
print a.island_metadata_list[0].gc_ratio
assert computed == expected
def test_single_cpg(self, algorithm):
seq_str = 'CG'
computed = algorithm(make_seq_record(seq_str), 2, 1, 2)
expected = make_algo_results(seq_str, [(0, 2, 1, 2)])
print computed.seq_record.features[0].extract(computed.seq_record.seq)
for a in [computed, expected]:
print a.island_metadata_list[0].gc_ratio
assert computed == expected
def test_island_at_end(self, algorithm):
seq_str = 'GCATAACGGTAATCTATCGTATCATATT'
computed = algorithm(make_seq_record(seq_str), 2, 0.5, 0.6)
expected = make_algo_results(
seq_str, [(6, 12, 0.5, 3), (17, 21, 0.5, 4)])
assert computed == expected
def test_island_at_end(self, algorithm):
seq_str = 'ATATATTATTCAACGAGG'
computed = algorithm(make_seq_record(seq_str), 5, 0.5, 0.6)
expected = make_algo_results(seq_str, [(10, 18, 0.625, 4 / 3)])
assert computed == expected
def test_island_in_middle(self, algorithm):
seq_str = 'ATATACACGGAATATT'
computed = algorithm(make_seq_record(seq_str), 4, 0.5, 0.6)
expected = make_algo_results(seq_str, [(5, 13, 0.5, 2)])
assert computed == expected
def test_island_at_beginning(self, algorithm):
seq_str = 'CGGATATATA'
computed = algorithm(make_seq_record(seq_str), 3, 0.5, 0.6)
expected = make_algo_results(seq_str, [(0, 6, 0.5, 3)])
assert computed == expected
def test_island_at_end(self, algorithm):
seq_str = 'GCATAACGGTAATCTATCGTATCATATT'
computed = algorithm(make_seq_record(seq_str), 2, 0.5, 0.6)
expected = make_algo_results(seq_str, [(6, 12, 0.5, 3),
(17, 21, 0.5, 4)])
assert computed == expected
def test_island_at_end(self, algorithm):
seq_str = 'ATATATTATTCAACGAGG'
computed = algorithm(make_seq_record(seq_str), 5, 0.5, 0.6)
expected = make_algo_results(seq_str, [(10, 18, 0.625, 4 / 3)])
assert computed == expected
def test_island_in_middle(self, algorithm):
seq_str = 'ATATACACGGAATATT'
computed = algorithm(make_seq_record(seq_str), 4, 0.5, 0.6)
expected = make_algo_results(seq_str, [(5, 13, 0.5, 2)])
assert computed == expected
def test_island_at_beginning(self, algorithm):
seq_str = 'CGGATATATA'
computed = algorithm(make_seq_record(seq_str), 3, 0.5, 0.6)
expected = make_algo_results(seq_str, [(0, 6, 0.5, 3)])
assert computed == expected
