def testMergedRecord_8_coInsDel(self):
# Variant 1
self.variant_1.pos = 5
self.variant_1.ref = "-"
self.variant_1.alt = ["GTGTG"]
# Variant 2
self.variant_2.pos = 5
self.variant_2.ref = "AA"
self.variant_2.alt = ["-"]
# Expected merge
self.expected_merge.pos = 5
self.expected_merge.ref = "AA"
self.expected_merge.alt = ["GTGTG"]
self.expected_merge.info = {
"AF": [0.06],
"MCO_QUAL": [10, 30],
"MCO_VAR": ["chr1:5=-/GTGTG", "chr1:5=AA/-"]
}
# Eval
with IdxFastaIO(self.tmp_fasta_path) as FH_ref:
observed_merge = mergedRecord(self.vcfio, self.variant_1,
self.variant_1.getName(),
self.variant_2,
self.variant_2.getName(), FH_ref)
self.assertEqual(strVariant(observed_merge),
strVariant(self.expected_merge))
def testMergedRecord_3_largeCloseSubstit(self):
# Variant 1
self.variant_1.pos = 5
self.variant_1.ref = "AAAT"
self.variant_1.alt = ["TGCA"]
# Variant 2
self.variant_2.pos = 9
self.variant_2.ref = "CT"
self.variant_2.alt = ["GG"]
# Expected merge
self.expected_merge.pos = 5
self.expected_merge.ref = "AAATCT"
self.expected_merge.alt = ["TGCAGG"]
self.expected_merge.info = {
"AF": [0.06],
"MCO_QUAL": [10, 30],
"MCO_VAR": ["chr1:5=AAAT/TGCA", "chr1:9=CT/GG"]
}
# Eval
with IdxFastaIO(self.tmp_fasta_path) as FH_ref:
observed_merge = mergedRecord(self.vcfio, self.variant_1,
self.variant_1.getName(),
self.variant_2,
self.variant_2.getName(), FH_ref)
self.assertEqual(strVariant(observed_merge),
strVariant(self.expected_merge))
def testMergedRecord_1_substit(self):
# Variant 1
self.variant_1.pos = 5
self.variant_1.ref = "A"
self.variant_1.alt = ["T"]
# Variant 2
self.variant_2.pos = 20
self.variant_2.ref = "G"
self.variant_2.alt = ["C"]
# Expected merge
self.expected_merge.pos = 5
self.expected_merge.ref = "AAATCTCGGCATGCCG"
self.expected_merge.alt = ["TAATCTCGGCATGCCC"]
self.expected_merge.info = {
"AF": [0.06],
"MCO_QUAL": [10, 30],
"MCO_VAR": ["chr1:5=A/T", "chr1:20=G/C"]
}
# Eval
with IdxFastaIO(self.tmp_fasta_path) as FH_ref:
observed_merge = mergedRecord(self.vcfio, self.variant_1,
self.variant_1.getName(),
self.variant_2,
self.variant_2.getName(), FH_ref)
self.assertEqual(strVariant(observed_merge),
strVariant(self.expected_merge))
def testMergedRecord_7_closeInsDel(self):
# Variant 1
self.variant_1.pos = 5
self.variant_1.ref = "-"
self.variant_1.alt = ["GTGTG"]
# Variant 2
self.variant_2.pos = 6
self.variant_2.ref = "AA"
self.variant_2.alt = ["-"]
# Expected merge
self.expected_merge.pos = 5
self.expected_merge.ref = "AAA"
self.expected_merge.alt = ["GTGTGA"]
self.expected_merge.info = {
"AF": [0.06],
"MCO_QUAL": [10, 30],
"MCO_VAR": ["chr1:5=-/GTGTG", "chr1:6=AA/-"]
}
# Eval
observed_merge = mergedRecord(self.vcfio, self.variant_1,
self.variant_1.getName(), self.variant_2,
self.variant_2.getName(), self.ref_seq)
self.assertEqual(strVariant(observed_merge),
strVariant(self.expected_merge))
def testMergedRecord_5_coDelIns(self):
# Variant 1
self.variant_1.pos = 5
self.variant_1.ref = "AAAT"
self.variant_1.alt = ["-"]
# Variant 2
self.variant_2.pos = 9
self.variant_2.ref = "-"
self.variant_2.alt = ["AGG"]
# Expected merge
self.expected_merge.pos = 5
self.expected_merge.ref = "AAAT"
self.expected_merge.alt = ["AGG"]
self.expected_merge.info = {
"AF": [0.06],
"MCO_QUAL": [10, 30],
"MCO_VAR": ["chr1:5=AAAT/-", "chr1:9=-/AGG"]
}
# Eval
observed_merge = mergedRecord(self.vcfio, self.variant_1,
self.variant_1.getName(), self.variant_2,
self.variant_2.getName(), self.ref_seq)
self.assertEqual(strVariant(observed_merge),
strVariant(self.expected_merge))
def testMergedRecord_2_largeSubstit(self):
# Variant 1
self.variant_1.pos = 5
self.variant_1.ref = "AAAT"
self.variant_1.alt = ["TGCA"]
# Variant 2
self.variant_2.pos = 10
self.variant_2.ref = "TC"
self.variant_2.alt = ["GG"]
# Expected merge
self.expected_merge.pos = 5
self.expected_merge.ref = "AAATCTC"
self.expected_merge.alt = ["TGCACGG"]
self.expected_merge.info = {
"AF": [0.06],
"MCO_QUAL": [10, 30],
"MCO_VAR": ["chr1:5=AAAT/TGCA", "chr1:10=TC/GG"]
}
# Eval
observed_merge = mergedRecord(self.vcfio, self.variant_1,
self.variant_1.getName(), self.variant_2,
self.variant_2.getName(), self.ref_seq)
self.assertEqual(strVariant(observed_merge),
strVariant(self.expected_merge))