def setUp(self):
self.contiguousRegions = ContiguousRegions('/dev/null', 'src',
'target', 100, '/tmp/',
10000, False, 0.25)
self.maxDiff = None
class ContiguousRegionsTestCase(unittest.TestCase):
def setUp(self):
self.contiguousRegions = ContiguousRegions('/dev/null', 'src',
'target', 100, '/tmp/',
10000, False, 0.25)
self.maxDiff = None
def test_mergeBlocks_noDups(self):
blocks = { 'seq1': [((0, 20, '+'), (20, 40, '+')),
((80, 100, '+'), (0, 20, '-')),
((20, 40, '+'), (50, 70, '+'))]
}
merged = { 'seq1': [((0, 20, '+'), [(20, 40, '+')]),
((20, 40, '+'), [(50, 70, '+')]),
((80, 100, '+'), [(0, 20, '-')])]
}
self.assertEqual(self.contiguousRegions.mergeBlocks(blocks), merged)
def test_mergeBlocks_simpleDuped(self):
blocks = {
# overlapping in the middle of a block
'seq1': [((0, 20, '+'), (20, 40, '+')),
((10, 15, '+'), (0, 5, '+')),
((20, 40, '+'), (50, 70, '+'))],
# overlapping and going past the end of a block
'seq2': [((0, 20, '+'), (20, 40, '+')),
((10, 30, '+'), (0, 20, '+'))]
}
merged = { 'seq1': [((0, 10, '+'), [(20, 30, '+')]),
((10, 15, '+'), [(30, 35, '+'), (0, 5, '+')]),
((15, 20, '+'), [(35, 40, '+')]),
((20, 40, '+'), [(50, 70, '+')])],
'seq2': [((0, 10, '+'), [(20, 30, '+')]),
((10, 20, '+'), [(30, 40, '+'), (0, 10, '+')]),
((20, 30, '+'), [(10, 20, '+')])]
}
self.assertEqual(self.contiguousRegions.mergeBlocks(blocks), merged)
def test_mergeBlocks_negativeStrandDuped(self):
blocks = {
# overlapping in the middle of a block
'seq1': [((0, 20, '+'), (20, 40, '-')),
((10, 15, '+'), (0, 5, '-')),
((20, 40, '+'), (50, 70, '-'))],
# overlapping and going past the end of a block
'seq2': [((0, 20, '+'), (20, 40, '-')),
((10, 30, '+'), (0, 20, '-'))]
}
merged = { 'seq1': [((0, 10, '+'), [(30, 40, '-')]),
((10, 15, '+'), [(25, 30, '-'), (0, 5, '-')]),
((15, 20, '+'), [(20, 25, '-')]),
((20, 40, '+'), [(50, 70, '-')])],
'seq2': [((0, 10, '+'), [(30, 40, '-')]),
((10, 20, '+'), [(20, 30, '-'), (10, 20, '-')]),
((20, 30, '+'), [(0, 10, '-')])]
}
self.assertEqual(self.contiguousRegions.mergeBlocks(blocks), merged)
def test_mergeBlocks_mixedStrandsDuped(self):
blocks = {
# overlapping in the middle of a block
'seq1': [((0, 20, '+'), (20, 40, '-')),
((10, 15, '+'), (0, 5, '+')),
((20, 40, '+'), (50, 70, '-'))],
# overlapping and going past the end of a block
'seq2': [((0, 20, '+'), (20, 40, '-')),
((10, 30, '+'), (0, 20, '+'))]
}
merged = { 'seq1': [((0, 10, '+'), [(30, 40, '-')]),
((10, 15, '+'), [(25, 30, '-'), (0, 5, '+')]),
((15, 20, '+'), [(20, 25, '-')]),
((20, 40, '+'), [(50, 70, '-')])],
'seq2': [((0, 10, '+'), [(30, 40, '-')]),
((10, 20, '+'), [(20, 30, '-'), (0, 10, '+')]),
((20, 30, '+'), [(10, 20, '+')])]
}
self.assertEqual(self.contiguousRegions.mergeBlocks(blocks), merged)
def test_mergeBlocks_tripled(self):
blocks = {
# stacking
'seq1': [((0, 20, '+'), (20, 40, '+')),
((0, 20, '+'), (70, 90, '-')),
((0, 20, '+'), (50, 70, '+'))],
# mixture of overlap types
'seq2': [((0, 20, '+'), (20, 40, '+')),
((10, 15, '+'), (60, 65, '-')),
((11, 30, '+'), (80, 99, '+'))]
}
merged = {
'seq1': [((0, 20, '+'), [(20, 40, '+'), (70, 90, '-'), (50, 70, '+')])],
'seq2': [((0, 10, '+'), [(20, 30, '+')]),
((10, 11, '+'), [(30, 31, '+'), (64, 65, '-')]),
((11, 15, '+'), [(31, 35, '+'), (60, 64, '-'), (80, 84, '+')]),
((15, 20, '+'), [(35, 40, '+'), (84, 89, '+')]),
((20, 30, '+'), [(89, 99, '+')])]
}
self.assertEqual(self.contiguousRegions.mergeBlocks(blocks), merged)
def test_mergeBlocks_staggered(self):
blocks = {
'seq1': [((0, 5, '+'), (0, 5, '+')),
((1, 6, '+'), (5, 10, '-')),
((2, 7, '+'), (10, 15, '+')),
((3, 8, '+'), (15, 20, '-')),
((4, 9, '+'), (20, 25, '-')),
((5, 10, '+'), (25, 30, '+'))]
}
merged = {
'seq1': [((0, 1, '+'), [(0, 1, '+')]),
((1, 2, '+'), [(1, 2, '+'), (9, 10, '-')]),
((2, 3, '+'), [(2, 3, '+'), (8, 9, '-'), (10, 11, '+')]),
((3, 4, '+'), [(3, 4, '+'), (7, 8, '-'), (11, 12, '+'), (19, 20, '-')]),
((4, 5, '+'), [(4, 5, '+'), (6, 7, '-'), (12, 13, '+'), (18, 19, '-'), (24, 25, '-')]),
((5, 6, '+'), [(5, 6, '-'), (13, 14, '+'), (17, 18, '-'), (23, 24, '-'), (25, 26, '+')]),
((6, 7, '+'), [(14, 15, '+'), (16, 17, '-'), (22, 23, '-'), (26, 27, '+')]),
((7, 8, '+'), [(15, 16, '-'), (21, 22, '-'), (27, 28, '+')]),
((8, 9, '+'), [(20, 21, '-'), (28, 29, '+')]),
((9, 10, '+'), [(29, 30, '+')])]
}
self.assertEqual(self.contiguousRegions.mergeBlocks(blocks), merged)
