def testSnpRanges(self):
BoundaryCheck.chrom = "NA"
b = SnpBoundaryCheck(snps=["rs1-rs500","rs600-rs650","rs987654321"])
self.assertFalse(b.NoExclusions())
self.assertTrue(b.valid)
self.assertFalse(b.TestBoundary(1, 10, "rs1"))
self.assertFalse(b.TestBoundary("NA", "NA", "rs750"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs1"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs50"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs1"))
# We don't really care which RS numbers we see, except for the boundaries
self.assertTrue(b.TestBoundary("NA", "NA", "rs1"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs500"))
self.assertFalse(b.TestBoundary("NA", "NA", "rs499"))
self.assertFalse(b.TestBoundary(22, 23001, "rs500"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs600"))
self.assertTrue(b.TestBoundary("NA", '23003', "rs625"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs20000"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs650"))
self.assertFalse(b.TestBoundary("NA", "NA", "rs650"))
self.assertFalse(b.TestBoundary(21, "NA", "rs987654321"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs987654321"))
def testSnpRangesWithExclusions(self):
BoundaryCheck.chrom = "NA"
b = SnpBoundaryCheck(snps=["rs1-rs500","1:600-1:650","1:987654321"])
b.ignored_rs = ["1:751","1:501"]
self.assertFalse(b.NoExclusions())
self.assertTrue(b.valid)
self.assertFalse(b.TestBoundary(1, "NA", "rs1"))
self.assertFalse(b.TestBoundary("NA", "NA", "rs750"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs1"))
self.assertFalse(b.TestBoundary("NA", "NA", "1:751"))
self.assertTrue(b.TestBoundary("NA", "NA", "1:50"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs1"))
# We don't really care which RS numbers we see, except for the boundaries
self.assertTrue(b.TestBoundary("NA", "NA", "rs1"))
self.assertFalse(b.TestBoundary("NA", "NA", "1:501"))
self.assertTrue(b.TestBoundary("NA", "NA", "rs500"))
self.assertFalse(b.TestBoundary("NA", "NA", "rs499"))
self.assertFalse(b.TestBoundary("NA", "NA", "rs500"))
self.assertTrue(b.TestBoundary("NA", "NA", "1:600"))
self.assertTrue(b.TestBoundary("NA", "NA", "1:625"))
self.assertTrue(b.TestBoundary("NA", "NA", "1:20000"))
self.assertTrue(b.TestBoundary("NA", "NA", "1:650"))
self.assertFalse(b.TestBoundary("NA", "NA", "1:650"))
self.assertFalse(b.TestBoundary(21, "NA", "1:987654321"))
self.assertTrue(b.TestBoundary("NA", "NA", "1:987654321"))
def testSnpRangesWithExclusions(self):
BoundaryCheck.chrom = 22
b = SnpBoundaryCheck(snps=["rs1-rs500","rs600-rs650","rs987654321"])
b.ignored_rs = ["rs751","rs501"]
self.assertFalse(b.NoExclusions())
self.assertTrue(b.valid)
self.assertFalse(b.TestBoundary(1, 10, "rs1"))
self.assertFalse(b.TestBoundary(22, 20000, "rs750"))
self.assertTrue(b.TestBoundary(22, 20001, "rs1"))
self.assertFalse(b.TestBoundary(22, 20002, "rs751"))
self.assertTrue(b.TestBoundary(22, 22003, "rs50"))
self.assertTrue(b.TestBoundary(22, 22005, "rs1"))
# We don't really care which RS numbers we see, except for the boundaries
self.assertTrue(b.TestBoundary(22, 22010, "rs1"))
self.assertFalse(b.TestBoundary(22, 22011, "rs501"))
self.assertTrue(b.TestBoundary(22, 22012, "rs500"))
self.assertFalse(b.TestBoundary(22, 23000, "rs499"))
self.assertFalse(b.TestBoundary(22, 23002, "rs500"))
self.assertTrue(b.TestBoundary(22, 23003, "rs600"))
self.assertTrue(b.TestBoundary(22, 23004, "rs625"))
self.assertTrue(b.TestBoundary(22, 23010, "rs20000"))
self.assertTrue(b.TestBoundary(22, 24000, "rs650"))
self.assertFalse(b.TestBoundary(22, 25000, "rs650"))
self.assertFalse(b.TestBoundary(21, 2500000, "rs987654321"))
self.assertTrue(b.TestBoundary(22, 2500000, "rs987654321"))