def test_cluster_gaps_singletonCluster(self):
length = 5
gaps = [MockGap(start, length) for start in [42,42,42]]
cluster_utility = DbscanClusterUtility()
actual_cluster_count = cluster_utility._cluster_gaps(gaps)
self.assertEquals(1, actual_cluster_count)
def test_cluster_standardClusterB(self):
#the distinct start,lengths from
#ENSMUST00000063084 for Sample 21791
gaps = [MockGap(start, length) for (start,length) in [
(811,26),(812,26), (813,26), (814,26), (815,26), (816,26),
(817,26), (818,26), (819,26), (820,26), (821,26), (918,67),
(919,67), (920,67), (921,67), (922,67), (1542,2), (1543,2),
(1544,2), (1545,2), (1546,2), (1547,2), (1754,2), (1755,2),
(1756,2), (1757,2), (1758,2), (1759,2),
]]
cluster_utility = DbscanClusterUtility()
actual_cluster_count = cluster_utility._cluster_gaps(gaps)
self.assertEquals(4, actual_cluster_count)
def test_cluster_gaps_simpleCluster(self):
#ENSMUST00000000305 for Samples 21786, 21797
#using eps=3, minSample=3, random_seed=42
length = 5
gaps = [MockGap(start, length) for start in [
192,192,192,
193,193,193,
194,194,194,
195,195,195,
196,196,196
]]
cluster_utility = DbscanClusterUtility()
actual_cluster_count = cluster_utility._cluster_gaps(gaps)
self.assertEquals(1, actual_cluster_count)
def test_cluster_standardClusterA(self):
#the distinct start,lengths from
#ENSMUST00000063084 for Samples 21786, 21797
gaps = [MockGap(start, length) for (start,length) in [
(811,26),(812,26),(813,26),(814,26),(815,26),(816,26),(817,26),
(818,26),(819,26),(820,26),(821,26),
(1554,2),(1555,2),(1556,2),(1557,2),(1558,2),
(773,146),(774,146),(775,146),(776,146),
(918,67),(919,67),(920,67),(921,67),(922,67),
(1324,2),(1325,2),(1326,2),(1327,2),(1328,2),
]]
cluster_utility = DbscanClusterUtility()
actual_cluster_count = cluster_utility._cluster_gaps(gaps)
self.assertEquals(5, actual_cluster_count)
def test_cluster_gaps_complexCluster(self):
#ENSMUST00000012259 for Samples 21786, 21797
#using eps=3, minSample=3, random_seed=42
#Individual reads were re-ordered to group with expected clusters
gaps = [MockGap(start, length) for (start,length) in [
(176,1216), (177,1216), #noise
(1516,27), (1516,24), (1516,24), (1516,27), (1517,27), (1517,24),
(1517,24), (1517,27), (1518,27), (1518,24), (1518,24),
(1518,27), (1519,27), (1519,24), (1519,24), (1519,27),
(1520,27), (1520,24), (1520,24), (1520,27), (1521,27),
(1521,24), (1521,24), (1521,27), (1522,27), (1522,24),
(1522,27), (1523,27), (1524,27), #cluster 0
(1142,249), (1142,249), (1142,249), (1142,249), (1142,249),
(1142,249), (1142,249), (1142,249), (1142,249), (1142,249),
(1142,249), (1143,249), (1143,249), (1143,249), (1143,249),
(1143,249), (1143,249), (1143,249), (1143,249), (1143,249),
(1144,249), (1144,249), (1144,249), (1144,249), (1144,249),
(1144,249), (1144,249), (1144,249), (1144,249), (1145,249),
(1145,249), (1145,249), (1145,249), (1145,249), (1145,249),
(1145,249), (1145,249), (1145,249), (1146,249), (1146,249),
(1146,249), (1146,249), (1146,249), (1146,249), (1146,249),
(1146,249), (1146,249), (1146,249), (1147,249), (1147,249),
(1147,249), (1147,249), (1147,249), (1147,249), (1147,249),
(1147,249), (1147,249), (1147,249), (1148,249), (1148,249),
(1148,249), (1148,249), (1148,249), (1148,249), (1148,249),
(1148,249), (1148,249), #cluster 1
(592,81), (593,81), (594,81), (595,81), (596,81), (597,81),
(598,81), (599,81),(600,81), (601,81), (602,81), (603,81),
(604,81), (605,81), (606,81), (607,81),(608,81), #cluster 2
(314,30), (314,30), (315,30), (315,30), (316,30), (316,30),
(317,30), (317,30), (318,30), (318,30), #cluster 3
(1780,4), (1781,4), (1782,4), (1783,4), (1784,4), (1785,4),
(1786,4), #cluster 4
(1388,43), (1389,43), (1390,43), (1391,43), (1392,43), (1393,43), (1394,43),
(1395,43), (1396,43), (1397,43), (1398,43), #cluster 5
(1142,129), (1142,129), (1143,129), (1143,129),(1145,129),
(1144,129), #cluster 6
(345,213), (345,213), (345,213), (345,213),
(345,213), (345,213), (345,213), (345,213), (345,213),
(345,213), (345,213), (345,213), (345,213), (345,213),
(346,213), (346,213), (346,213), (346,213), (346,213),
(346,213), (346,213), (346,213), (346,213), (346,213),
(346,213), (346,213), (346,213), (346,213), (346,213),
(346,213), (347,213), (347,213), (347,213), (347,213),
(347,213), (347,213), (347,213), (347,213), (347,213),
(347,213), (347,213), (347,213), (347,213), (347,213),
(347,213), #cluster 7
(175,88), (175,88), (176,88), (176,88), (177,88), #cluster 8
(3053,2), (3054,2), (3055,2), (3056,2), #cluster 9
(2072,2), (2073,2), (2074,2), (2075,2), (2076,2), #cluster 10
(583,4), (584,4), (585,4), #cluster 11
(558,713), (559,713), (560,713), (561,713), #cluster 12
(2240,99), (2241,99), (2242,99), (2243,99), (2244,99), (2245,99),
(2246,99), #cluster 13
(344,926), (345,926), (346,926), (347,926), (348,926), #cluster 14
(1912,64), (1913,64),(1914,64), (1915,64), #cluster 15
(1089,2), (1090,2), (1091,2), (1092,2), (1093,2), #cluster 16
(363,2), (364,2), (365,2), (366,2), (367,2), #cluster 17
]]
cluster_utility = DbscanClusterUtility()
actual_cluster_count = cluster_utility._cluster_gaps(gaps)
self.assertEquals(18, actual_cluster_count)