def testAddAllele(self):
mut = Mutation()
for chrom in range(4):
mut.addAllele(chrom, 0)
self.assertEqual(mut.numAlleles(chrom), 2)
mut.addAllele(0, 0)
self.assertEqual(mut.numAlleles(0), 3)
def setUp(self):
self.mut = Mutation()
self.mut._hist[0] = {0: [None],
1: [None, 0],
2: [None, 0, 1],
3: [None, 0],
4: [None, 0, 3],
5: [None, 0, 1, 2],
6: [None, 0, 1, 2],
7: [None, 0, 1, 2, 5],
8: [None, 0, 1, 2, 6]}
self.mut._max[0] = len(self.mut.history(0))
def testHistory(self):
mut = Mutation()
mut.addAllele(0, 0)
mut.addAllele(0, 0)
mut.addAllele(0, 2)
mut.addAllele(0, 2)
hist = mut.history(0)
self.assertEqual(mut.numAlleles(0), 5)
self.assertEqual(mut.history(0),
{0: [None],
1: [None, 0],
2: [None, 0],
3: [None, 0, 2],
4: [None, 0, 2]})
def testInit(self):
mut = Mutation()
for chrom in range(4):
self.assertEqual(mut.numAlleles(chrom), 1)
self.assertEqual(mut.history(chrom), {0: [None]})
class TestMutation(unittest.TestCase):
def setUp(self):
self.mut = Mutation()
self.mut._hist[0] = {0: [None],
1: [None, 0],
2: [None, 0, 1],
3: [None, 0],
4: [None, 0, 3],
5: [None, 0, 1, 2],
6: [None, 0, 1, 2],
7: [None, 0, 1, 2, 5],
8: [None, 0, 1, 2, 6]}
self.mut._max[0] = len(self.mut.history(0))
def testInit(self):
mut = Mutation()
for chrom in range(4):
self.assertEqual(mut.numAlleles(chrom), 1)
self.assertEqual(mut.history(chrom), {0: [None]})
def testAddAllele(self):
mut = Mutation()
for chrom in range(4):
mut.addAllele(chrom, 0)
self.assertEqual(mut.numAlleles(chrom), 2)
mut.addAllele(0, 0)
self.assertEqual(mut.numAlleles(0), 3)
def testHistory(self):
mut = Mutation()
mut.addAllele(0, 0)
mut.addAllele(0, 0)
mut.addAllele(0, 2)
mut.addAllele(0, 2)
hist = mut.history(0)
self.assertEqual(mut.numAlleles(0), 5)
self.assertEqual(mut.history(0),
{0: [None],
1: [None, 0],
2: [None, 0],
3: [None, 0, 2],
4: [None, 0, 2]})
def testClear(self):
self.mut.addAllele(0, 0)
self.mut.clear()
for chrom in range(4):
self.assertEqual(self.mut.numAlleles(chrom), 1)
self.assertEqual(self.mut.history(chrom), {0: [None]})
def testPruneMonomorphic(self):
self.mut.prune(0, [7])
self.assertEqual(self.mut.history(0),
{0: [None]})
self.assertEqual(self.mut.numAlleles(0), 1)
def testPruneRecentSplit(self):
self.mut.prune(0, [7, 8])
self.assertEqual(self.mut.history(0),
{3: [None, 0, 1],
4: [None, 0, 2]})
self.assertEqual(self.mut.numAlleles(0), 5)
def testPruneAncentSplit(self):
self.mut.prune(0, [3, 7])
self.assertEqual(self.mut.history(0),
{3: [None, 0],
5: [None, 0, 1, 2, 4]})
self.assertEqual(self.mut.numAlleles(0), 6)
def testPairwiseDistance(self):
expected = {(0, 1): 1,
(0, 2): 2,
(0, 3): 1,
(0, 4): 2,
(0, 5): 3,
(0, 6): 3,
(0, 7): 4,
(0, 8): 4,
(1, 2): 1,
(1, 3): 2,
(1, 4): 3,
(1, 5): 2,
(1, 6): 2,
(1, 7): 3,
(1, 8): 3,
(2, 3): 3,
(2, 4): 4,
(2, 5): 1,
(2, 6): 1,
(2, 7): 2,
(2, 8): 2,
(3, 4): 1,
(3, 5): 4,
(3, 6): 4,
(3, 7): 5,
(3, 8): 5,
(4, 5): 5,
(4, 6): 5,
(4, 7): 6,
(4, 8): 6,
(5, 6): 2,
(5, 7): 1,
(5, 8): 3,
(6, 7): 3,
(6, 8): 1,
(7, 8): 4}
self.assertEqual(self.mut.pairwiseDistance(0), expected)
def testPairwiseDistanceAfterPrune(self):
self.mut.prune(0, [7, 8])
expected = {(3, 4): 4}
self.assertEqual(self.mut.pairwiseDistance(0), expected)
