def testBoundaryX(self):
BoundaryCheck.set_chrom('X')
b = BoundaryCheck()
self.assertEqual(23, BoundaryCheck.chrom)
self.assertEqual('X', BoundaryCheck.chrom_name)
self.assertTrue(b.TestBoundary('x', 100, "rs100"))
self.assertTrue(b.TestBoundary('X', 1000, "rs1000"))
self.assertTrue(b.TestBoundary(23, 1000, "rs1000"))
self.assertFalse(b.TestBoundary('Y', 100, "rs100"))
def testBoundaryInitBP(self):
BoundaryCheck.chrom = 1
b = BoundaryCheck(bp=[10000, 500000])
self.assertFalse(b.NoExclusions())
self.assertTrue(b.valid)
self.assertEqual(False, b.TestBoundary(1, 500, ""))
self.assertEqual(True, b.TestBoundary(1, 10000, ""))
self.assertEqual(True, b.TestBoundary(1, 500000, ""))
self.assertEqual(True, b.TestBoundary(1, 250000, ""))
self.assertEqual(False, b.TestBoundary(2, 250000, ""))
self.assertEqual(False, b.TestBoundary(10, 10000, ""))
def testBoundaryInitMB(self):
BoundaryCheck.chrom = 10
b = BoundaryCheck(mb=[1,3])
self.assertTrue(b.valid)
self.assertFalse(b.NoExclusions())
self.assertTrue(b.TestBoundary(10, 1000000, ""))
self.assertTrue(b.TestBoundary(10, 1200000, ""))
self.assertTrue(b.TestBoundary(10, 3000000, ""))
self.assertFalse(b.TestBoundary(10, 3000001, ""))
self.assertFalse(b.TestBoundary(10, 999999, ""))
self.assertFalse(b.TestBoundary(1, 1000500, ""))
def testBoundaryChr10(self):
BoundaryCheck.set_chrom('chr10')
b = BoundaryCheck(mb=[1,3])
self.assertTrue(b.valid)
self.assertFalse(b.NoExclusions())
self.assertTrue(b.TestBoundary(10, 1000000, ""))
self.assertTrue(b.TestBoundary(10, 1200000, ""))
self.assertTrue(b.TestBoundary(10, 3000000, ""))
self.assertFalse(b.TestBoundary(10, 3000001, ""))
self.assertFalse(b.TestBoundary(10, 999999, ""))
self.assertFalse(b.TestBoundary(1, 1000500, ""))
def testBoundaryInitKB(self):
BoundaryCheck.chrom = 5
b = BoundaryCheck(kb=[20, 50])
self.assertFalse(b.NoExclusions())
self.assertEqual(True, b.valid)
self.assertEqual(False, b.TestBoundary(5, 15000, ""))
self.assertEqual(True, b.TestBoundary(5, 20000, ""))
self.assertEqual(True, b.TestBoundary(5, 30000, ""))
self.assertEqual(True, b.TestBoundary(5, 50000, ""))
self.assertEqual(False, b.TestBoundary(5, 50001, ""))
self.assertEqual(False, b.TestBoundary(1, 25000, ""))
self.assertEqual(False, b.TestBoundary(10, 20000, ""))
def testDefaultBoundaryInitialization(self):
# By default, it will identify as invalid, since it didn't find any boundaries
# This is just for simplifying command line parsing
BoundaryCheck.chrom = -1
b = BoundaryCheck()
self.assertEqual(False, b.valid)
# At this point, this should any valid chromosome/position combination
self.assertTrue(b.TestBoundary(1, 100, ""))
self.assertTrue(True, b.TestBoundary(10, 1000000, ""))
self.assertTrue(True, b.TestBoundary(25, 10000, ""))
# We should test that our short circuit functionality works
self.assertTrue(b.NoExclusions())
def testBoundaryInitBPWithExclusions(self):
BoundaryCheck.chrom = 1
b = BoundaryCheck(bp=[10000, 500000])
b.LoadExclusions(["rs12345", "rs234567", "rs345678"])
self.assertFalse(b.NoExclusions())
self.assertTrue(b.valid)
self.assertFalse(b.TestBoundary(1, 500, ""))
self.assertTrue(b.TestBoundary(1, 10000, ""))
self.assertFalse(b.TestBoundary(1, 10010, "rs12345"))
self.assertTrue(b.TestBoundary(1, 24000, "rs9876"))
self.assertFalse(b.TestBoundary(1, 25000, "rs234567"))
self.assertTrue(b.TestBoundary(1, 250000, ""))
self.assertTrue(b.TestBoundary(1, 500000, ""))
self.assertFalse(b.TestBoundary(2, 250000, ""))
self.assertFalse(b.TestBoundary(10, 10000, ""))
def testBoundaryInitBPWithInclusions(self):
BoundaryCheck.chrom = 1
b = BoundaryCheck(bp=[10000, 500000])
b.LoadSNPs(["rs12345", "rs23456"])
self.assertFalse(b.NoExclusions())
self.assertTrue(b.valid)
self.assertEqual(False, b.TestBoundary(1, 500, ""))
self.assertEqual(True, b.TestBoundary(1, 10000, ""))
self.assertEqual(True, b.TestBoundary(1, 500000, ""))
self.assertEqual(True, b.TestBoundary(1, 250000, ""))
self.assertEqual(False, b.TestBoundary(2, 250000, ""))
self.assertEqual(False, b.TestBoundary(10, 10000, ""))
self.assertTrue(b.TestBoundary(1, 1000000, "rs12345"))
self.assertTrue(b.TestBoundary(1, 1200000, "rs23456"))
self.assertFalse(b.TestBoundary(1, 1200011, "rs345678"))
def testBoundaryExceedPos(self):
BoundaryCheck.chrom = 10
b = BoundaryCheck(mb=[1,3])
self.assertTrue(b.valid)
self.assertFalse(b.NoExclusions())
self.assertFalse(b.TestBoundary(10, 100, ""))
self.assertFalse(b.beyond_upper_bound)
self.assertTrue(b.TestBoundary(10, 1000000, ""))
self.assertFalse(b.beyond_upper_bound)
self.assertTrue(b.TestBoundary(10, 1200000, ""))
self.assertFalse(b.beyond_upper_bound)
self.assertTrue(b.TestBoundary(10, 3000000, ""))
self.assertFalse(b.beyond_upper_bound)
self.assertFalse(b.TestBoundary(10, 3000001, ""))
self.assertTrue(b.beyond_upper_bound)
self.assertFalse(b.TestBoundary(10, 999999, ""))
self.assertFalse(b.beyond_upper_bound)