def test_hg38_negStrand_simple3utr(self):
line = "17\t43044315\t438907\tT\tA\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.+1363A>T', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_dup3utr(self):
line = "17\t43044804\t803399\tC\tCTTTTTTTTT\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.+865_+873dup9', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_fsdelins(self):
line = "17\t43045707\trs483353103\tT\tGGATCC\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5563delinsGGATCC_p.Ile1855GlyfsTer69', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_fsdup(self):
line = "17\t43045708\t949924\tC\tCAGGT\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5558_5561dupACCT_p.Ile1855ProfsTer26', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_simplestop(self):
line = "17\t43045711\t55630\tG\tC\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5559C>G_p.Tyr1853Ter', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_fsdel(self):
line = "17\t43093140\trs80357695\tTTC\tT\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.2389_2390delGA_p.Glu797ThrfsTer3', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_simple_nc(self):
line = "17\t43045705\t869060\tT\tA\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5565A>T_p.Ile1855=', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_simplemissense(self):
line = "17\t43051071\tVCV000017694.14\tA\tC\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5324T>G_p.Met1775Arg', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_delinsSpliceDonor(self):
line = "17\t43047641\t267604\tAC\tGG\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5467+1_5467+2delinsCC', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_dupSpliceDonor(self):
line = "17\t43063871\t55424\tT\tTA\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5152+2dupT', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_simpleSpliceDonor(self):
line = "17\t43047641\t125851\tA\tG\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5467+2T>C', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_delSpliceAcceptor(self):
line = "17\t43045802\t632610\tGC\tG\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5468-1delG', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_dupSpliceAcceptor(self):
line = "17\t43045749\t267605\tT\tTGTCCAACACCCACTCTCGGGTCACCACAGGTGCCTCACACATCTGCCCAATTGCTGGAGACAGA\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5468-11_5520dup64_p.Ala1843SerfsTer8', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_simpleSpliceAcceptor(self):
line = "17\t43045803\t864908\tC\tA\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.5468-1G>T', rec.variants[0].getFlag('CSN'))
def test_hg38_negStrand_delins3utr(self):
line = "17\t43044804\t323411\tCTT\tCG\t.\t.\t.\tGT\t0/1\n"
rec = core.Record(line, self.options, None)
rec.annotate(self.ensembl, None, self.reference, None)
rec.variants[0].getFlag('CSN')
self.assertEqual('c.+872_+873delinsC', rec.variants[0].getFlag('CSN'))
