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))