def testIndelOrSvMatch(self):
# variant types don't match
pred_var = Variant(10, 'A', ['AAA'], VARIANT_TYPE.INDEL_INS,
GENOTYPE_TYPE.HOM_VAR)
true_var = Variant(10, 'ACGT', ['ATGC'], VARIANT_TYPE.INDEL_OTH,
GENOTYPE_TYPE.HOM_VAR)
self.assertFalse(indel_or_sv_match(pred_var, true_var, EPS_BP,
EPS_LEN))
# pred var too far away from true var
pred_var = Variant(40, 'A', ['AAA'], VARIANT_TYPE.INDEL_INS,
GENOTYPE_TYPE.HOM_VAR)
true_var = Variant(20, 'A', ['AAA'], VARIANT_TYPE.INDEL_INS,
GENOTYPE_TYPE.HOM_VAR)
self.assertFalse(indel_or_sv_match(pred_var, true_var, EPS_BP,
EPS_LEN))
# pred pos off from true pos but within tolerance
pred_var = Variant(18, 'A', ['AAA'], VARIANT_TYPE.INDEL_INS,
GENOTYPE_TYPE.HOM_VAR)
true_var = Variant(20, 'A', ['AAA'], VARIANT_TYPE.INDEL_INS,
GENOTYPE_TYPE.HOM_VAR)
self.assertTrue(indel_or_sv_match(pred_var, true_var, EPS_BP, EPS_LEN))
# pred gains too different from true gains
pred_var = Variant(20, 'A', ['AAAAAAAAAAAAAAA'],
VARIANT_TYPE.INDEL_INS, GENOTYPE_TYPE.HOM_VAR)
true_var = Variant(20, 'A', ['AAA'], VARIANT_TYPE.INDEL_INS,
GENOTYPE_TYPE.HOM_VAR)
self.assertFalse(indel_or_sv_match(pred_var, true_var, EPS_BP,
EPS_LEN))
# pred gains off from true gains but within tolerance
pred_var = Variant(20, 'A', ['AAAAA'], VARIANT_TYPE.INDEL_INS,
GENOTYPE_TYPE.HOM_VAR)
true_var = Variant(20, 'A', ['AAA'], VARIANT_TYPE.INDEL_INS,
GENOTYPE_TYPE.HOM_VAR)
self.assertTrue(indel_or_sv_match(pred_var, true_var, EPS_BP, EPS_LEN))
def testInsertionVariant(self):
testVar = Variant(10,'A',['AAAA'],VARIANT_TYPE.INDEL_INS,GENOTYPE_TYPE.HET)
self.assertEqual(testVar.gains,[3])
self.assertEqual(testVar.losses,[0])
self.assertFalse(testVar.overlaps_allele(9))
self.assertTrue(testVar.overlaps_allele(10))
self.assertFalse(testVar.overlaps_allele(11))
def testOverlapsVariant(self):
snpVar = Variant(10,'A',['C'],VARIANT_TYPE.SNP,GENOTYPE_TYPE.HET)
indelVar = Variant(7,'AAAAAAAA',['A'],VARIANT_TYPE.INDEL_DEL,GENOTYPE_TYPE.HET)
self.assertTrue(snpVar.strictly_overlaps_var(indelVar))
self.assertTrue(indelVar.strictly_overlaps_var(snpVar))
snpVar2 = Variant(2,'C',['T'],VARIANT_TYPE.SNP,GENOTYPE_TYPE.HET)
self.assertFalse(snpVar2.strictly_overlaps_var(indelVar))
self.assertFalse(indelVar.strictly_overlaps_var(snpVar2))
def testSnpVariant(self):
testVar = Variant(10,'A',['C'],VARIANT_TYPE.SNP,GENOTYPE_TYPE.HET)
self.assertEqual(testVar.gains,[0])
self.assertEqual(testVar.losses,[0])
