def test_can_handle_single_run_plus_other(self):
content = '...HHHHHEEE'
results = parse._extract_secondary_runs(content, ss_type='H', run_length=5, at_least=5)
self.assertEqual(len(results), 1)
result = results[0]
self.assertEqual(result.start, 3)
self.assertEqual(result.end, 8)
def test_can_handle_multiple_runs(self):
content = '...HHHHH...HHHHH...'
results = parse._extract_secondary_runs(content, ss_type='H', run_length=5, at_least=5)
self.assertEqual(len(results), 2)
self.assertEqual(results[0].start, 3)
self.assertEqual(results[0].end, 8)
self.assertEqual(results[1].start, 11)
self.assertEqual(results[1].end, 16)
def test_can_handle_single_run(self):
content = "HHHHH"
results = parse._extract_secondary_runs(
content, ss_type="H", run_length=5, at_least=5, first_residue=0
)
self.assertEqual(len(results), 1)
result = results[0]
self.assertEqual(result.start, 0)
self.assertEqual(result.end, 5)
def test_can_handle_single_run_plus_other(self):
content = "...HHHHHEEE"
results = parse._extract_secondary_runs(
content, ss_type="H", run_length=5, at_least=5, first_residue=0
)
self.assertEqual(len(results), 1)
result = results[0]
self.assertEqual(result.start, 3)
self.assertEqual(result.end, 8)
def test_can_handle_single_run(self):
content = 'HHHHH'
results = parse._extract_secondary_runs(content,
ss_type='H',
run_length=5,
at_least=5)
self.assertEqual(len(results), 1)
result = results[0]
self.assertEqual(result.start, 0)
self.assertEqual(result.end, 5)
def test_can_handle_multiple_runs(self):
content = "...HHHHH...HHHHH..."
results = parse._extract_secondary_runs(
content, ss_type="H", run_length=5, at_least=5, first_residue=0
)
self.assertEqual(len(results), 2)
self.assertEqual(results[0].start, 3)
self.assertEqual(results[0].end, 8)
self.assertEqual(results[1].start, 11)
self.assertEqual(results[1].end, 16)
def test_can_handle_at_least(self):
content = "...HHHHH..."
results = parse._extract_secondary_runs(
content, ss_type="H", run_length=5, at_least=4, first_residue=0
)
self.assertEqual(len(results), 3)
self.assertEqual(results[0].start, 2)
self.assertEqual(results[0].end, 7)
self.assertEqual(results[1].start, 3)
self.assertEqual(results[1].end, 8)
self.assertEqual(results[2].start, 4)
self.assertEqual(results[2].end, 9)
def test_can_handle_at_least(self):
content = '...HHHHH...'
results = parse._extract_secondary_runs(content,
ss_type='H',
run_length=5,
at_least=4)
self.assertEqual(len(results), 3)
self.assertEqual(results[0].start, 2)
self.assertEqual(results[0].end, 7)
self.assertEqual(results[1].start, 3)
self.assertEqual(results[1].end, 8)
self.assertEqual(results[2].start, 4)
self.assertEqual(results[2].end, 9)