def testVariantsFromAlignment4(self): a = PairwiseAlignment("GA-TACA", "GATTACA") qvs = [0, 0, 1, 0, 0, 0, 0] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) EQ([ Variant(1, 1002, 1002, "", "T", confidence=1, refPrev="A", readPrev="A") ], vs)
def testVariantsFromAlignment5(self): a = PairwiseAlignment("-ATTACA", "GATTACA") qvs = [1, 0, 0, 0, 0, 0, 0] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) EQ([ Variant(1, 1000, 1000, "", "G", confidence=1, refPrev="N", readPrev="N") ], vs)
def testDeletionConfidence1(self): a = PairwiseAlignment("GATTACA", "GATTAC-") qvs = [0, 0, 0, 0, 0, 1] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) EQ([ Variant(1, 1006, 1007, "A", "", confidence=1, refPrev="C", readPrev="C") ], vs)
def testLongDeletion(self): a = PairwiseAlignment("GACCCCCTTACA", "GA-----TTACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) assert_equal([Variant(1, 1002, 1007, "CCCCC", "")], vs)
def testVariantsFromAlignment4(self): a = PairwiseAlignment("GA-TACA", "GATTACA") qvs = [0, 0, 1, 0, 0, 0, 0] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) assert_equal([Variant(1, 1002, 1002, "", "T", confidence=1)], vs)
def testVariantsFromAlignment3(self): a = PairwiseAlignment("GATTACA", "GAGGACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) EQ([ Variant(1, 1002, 1004, "TT", "GG", refPrev="A", readPrev="A") ], vs)
def testDeletionConfidence3(self): a = PairwiseAlignment("AT", "--") qvs = [] vs = utils.variantsFromAlignment(a, (1, 1000, 1002), qvs) assert_equal([ Variant(1, 1000, 1002, "AT", "") ], vs)
def testNoCallBasesInReference1(self): a = PairwiseAlignment("GATTNGATT", "GAGGATATT") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) EQ([ Variant(1, 1002, 1004, "TT", "GG", refPrev="A", readPrev="A"), Variant(1, 1005, 1006, "G", "T", refPrev="N", readPrev="A") ], vs)
def testVariantsFromAlignment4(self): a = PairwiseAlignment("GA-TACA", "GATTACA") qvs = [0, 0, 1, 0, 0, 0, 0] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) assert_equal([ Variant(1, 1002, 1002, "", "T", confidence=1) ], vs)
def testVariantsFromAlignment1(self): a = PairwiseAlignment("GATTACA", "GAT-ACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) assert_equal([Variant(1, 1003, 1004, "T", "")], vs)
def testDeletionConfidence3(self): a = PairwiseAlignment("AT", "--") qvs = [] vs = utils.variantsFromAlignment(a, (1, 1000, 1002), qvs) EQ([Variant(1, 1000, 1002, "AT", "", refPrev="N", readPrev="N")], vs)
def testDeletionConfidence2(self): a = PairwiseAlignment("GATTACA", "-ATTACA") qvs = [1, 0, 0, 0, 0, 0] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) EQ([ Variant(1, 1000, 1001, "G", "", confidence=1, refPrev="N", readPrev="N") ], vs)
def testDeletionConfidence3(self): a = PairwiseAlignment("AT", "--") qvs = [] vs = utils.variantsFromAlignment(a, (1, 1000, 1002), qvs) EQ([ Variant(1, 1000, 1002, "AT", "", refPrev="N", readPrev="N") ], vs)
def testTwoSubstitutions(self): a = PairwiseAlignment("GATTACA", "GAGTAGA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) EQ([ Variant(1, 1002, 1003, "T", "G", refPrev="A", readPrev="A"), Variant(1, 1005, 1006, "C", "G", refPrev="A", readPrev="A") ], vs)
def testLongDeletion(self): a = PairwiseAlignment("GACCCCCTTACA", "GA-----TTACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) EQ([ Variant(1, 1002, 1007, "CCCCC", "", refPrev="A", readPrev="A") ], vs)
def testDeletionConfidence1(self): a = PairwiseAlignment("GATTACA", "GATTAC-") qvs = [0, 0, 0, 0, 0, 1] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) assert_equal([Variant(1, 1006, 1007, "A", "", confidence=1)], vs)
def testVariantsFromAlignment3(self): a = PairwiseAlignment("GATTACA", "GAGGACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) EQ([Variant(1, 1002, 1004, "TT", "GG", refPrev="A", readPrev="A")], vs)
def testDeletionConfidence2(self): a = PairwiseAlignment("GATTACA", "-ATTACA") qvs = [1, 0, 0, 0, 0, 0] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) assert_equal([Variant(1, 1000, 1001, "G", "", confidence=1)], vs)
def testLongDeletion(self): a = PairwiseAlignment("GACCCCCTTACA", "GA-----TTACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) assert_equal([ Variant(1, 1002, 1007, "CCCCC", "") ], vs)
def testDeletionConfidence3(self): a = PairwiseAlignment("AT", "--") qvs = [] vs = utils.variantsFromAlignment(a, (1, 1000, 1002), qvs) assert_equal([Variant(1, 1000, 1002, "AT", "")], vs)
def testDeletionConfidence1(self): a = PairwiseAlignment("GATTACA", "GATTAC-") qvs = [0, 0, 0, 0, 0, 1] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) assert_equal([ Variant(1, 1006, 1007, "A", "", confidence=1) ], vs)
def testNoCallBasesInReference1(self): a = PairwiseAlignment("GATTNGATT", "GAGGATATT") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) assert_equal([ Variant(1, 1002, 1004, "TT", "GG"), Variant(1, 1005, 1006, "G", "T") ], vs)
def testTwoSubstitutions(self): a = PairwiseAlignment("GATTACA", "GAGTAGA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) assert_equal([ Variant(1, 1002, 1003, "T", "G"), Variant(1, 1005, 1006, "C", "G") ], vs)
def testLongDeletion(self): a = PairwiseAlignment("GACCCCCTTACA", "GA-----TTACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) EQ([Variant(1, 1002, 1007, "CCCCC", "", refPrev="A", readPrev="A")], vs)
def testDeletionConfidence2(self): a = PairwiseAlignment("GATTACA", "-ATTACA") qvs = [1, 0, 0, 0, 0, 0] vs = utils.variantsFromAlignment(a, (1, 1000, 2000), qvs) assert_equal([ Variant(1, 1000, 1001, "G", "", confidence=1) ], vs)
def testVariantsFromAlignment1(self): a = PairwiseAlignment("GATTACA", "GAT-ACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) EQ([Variant(1, 1003, 1004, "T", "", refPrev="T", readPrev="T")], vs)
def testVariantsFromAlignment1(self): a = PairwiseAlignment("GATTACA", "GAT-ACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) assert_equal([ Variant(1, 1003, 1004, "T", "") ], vs)
def testVariantsFromAlignment1(self): a = PairwiseAlignment("GATTACA", "GAT-ACA") vs = utils.variantsFromAlignment(a, (1, 1000, 2000)) EQ([ Variant(1, 1003, 1004, "T", "", refPrev="T", readPrev="T") ], vs)