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 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 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 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 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)