def test_check_consistency_fail1(self):
"""
No transcript interval.
"""
intervals = [create_interval_from_list(['1', '.', 'UTR5', '1', '9', '.', '+', '.', '.'])]
message = "No transcript interval in list of intervals."
with self.assertRaisesRegex(ValueError, message):
segment._check_consistency(intervals)
def test_check_consistency_fail3(self):
"""
Unallowed order of types.
"""
intervals = list_to_intervals([
['1', '.', 'transcript', '1', '100', '.', '+', '.', '.'],
['1', '.', 'UTR3', '1', '49', '.', '+', '.', '.'],
['1', '.', 'CDS', '50', '100', '.', '+', '.', '.'],
])
with self.assertRaises(AssertionError):
segment._check_consistency(intervals)
def test_check_consistency_fail2(self):
"""
Overlaping intervals.
"""
intervals = list_to_intervals([
['1', '.', 'transcript', '1', '100', '.', '+', '.', '.'],
['1', '.', 'UTR5', '1', '50', '.', '+', '.', '.'],
['1', '.', 'CDS', '50', '100', '.', '+', '.', '.'],
])
with self.assertRaises(AssertionError):
segment._check_consistency(intervals)
def test_check_consistency_pass(self): # pylint: disable=no-self-use
intervals = list_to_intervals([
['1', '.', 'transcript', '1', '100', '.', '+', '.', '.'],
['1', '.', 'UTR5', '1', '9', '.', '+', '.', '.'],
['1', '.', 'CDS', '10', '49', '.', '+', '.', '.'],
['1', '.', 'intron', '50', '59', '.', '+', '.', '.'],
['1', '.', 'CDS', '60', '89', '.', '+', '.', '.'],
['1', '.', 'UTR3', '90', '100', '.', '+', '.', '.'],
])
# If no AssertionError is raised, this is succes:
segment._check_consistency(intervals)