def test_undirected_SNV(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "ANY",
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, self.negative_transcript).get_vcf_row()
def test_directed_SNV_exists_missense(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "MISSENSE",
"START": 72121517
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, self.positive_transcript)
def test_undirected_SNV_stoploss_exists(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "STOPLOSS",
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, self.negative_transcript).get_vcf_row()
self.assertIn(snv['pos'], ["64048166", "64048167", "64048168"])
def test_directed_SNV_stoploss_false(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "STOPLOSS",
"START": 64048164
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(Exception):
snv = SNV(snv, self.negative_transcript)
def test_directed_SNV_not_exists_missense(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "MISSENSE",
"START": 64048502
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(Exception):
snv = SNV(snv, self.negative_transcript)
def test_wrong_type_impact(self):
snv = {
"TYPE": "SNV",
"REGION": "INTRONIC",
"IMPACT": {
"SNV_TYPE": "WRONG",
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
SNV(snv, self.transcript)
def test_directed_SNV_false(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "NONSENSE",
"START": 72121517
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(Exception):
snv = SNV(snv, self.positive_transcript)
def test_non_coding_incorrect_impact(self):
snv = {
"TYPE": "SNV",
"REGION": "INTRONIC",
"IMPACT": {
"SNV_TYPE": "MISSENSE",
"START": 72121999
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
snv = SNV(snv, self.positive_transcript)
def test_directed_SNV_exists_SYNONYMOUS(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "SYNONYMOUS",
"START": 64048502
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, self.negative_transcript).get_vcf_row()
self.assertEqual(snv['ref'], "C")
self.assertIn(snv['alt'], ["A", "G", "T"])
def test_directed_SNV_exists_nonsense(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "NONSENSE",
"START": 64048519
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, self.negative_transcript).get_vcf_row()
self.assertEqual(snv['ref'], "C")
self.assertEqual(snv['alt'], "A")
def test_directed_SNV_exists_single_replacement(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "G",
"START": 64048520
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, self.negative_transcript).get_vcf_row()
self.assertEqual(snv['ref'], "C")
self.assertEqual(snv['alt'], "G")
def test_basic_non_coding(self):
snv = {
"TYPE": "SNV",
"REGION": "INTRONIC",
"IMPACT": {
"SNV_TYPE": "A",
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, self.positive_transcript)
row = snv.get_vcf_row()
self.assertEqual(row["alt"], "A")
class MutationMethods(unittest.TestCase):
time.sleep(1)
XKR8_uid = get_all_transcripts("XKR8", "grch38")[0]["qualifiers"]["uid"]
transcript = Transcript(XKR8_uid, "grch38")
snv = {
"TYPE": "SNV",
"REGION": "INTRONIC",
"IMPACT": {
"SNV_TYPE": "A",
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, transcript)
# test 3
def test_nonsense_exists(self):
self.assertEqual(self.snv.nonsense_mutation("TAT", 2), "A")
# test 4
def test_nonsense_not_exists(self):
self.assertFalse(self.snv.nonsense_mutation("TAT", 1))
# test 5
def test_misssense_false(self):
self.assertFalse(self.snv.missense_mutation("TAT", 2))
# test 6
def test_misssense_exists(self):
self.assertIn(self.snv.missense_mutation("CAC", 2), ["G", "A"])
# test 7
def test_synonymous_exists(self):
self.assertFalse(self.snv.synonymous_mutation("TGG", 2))
# test 8
def test_synonymous_false(self):
self.assertEqual(self.snv.synonymous_mutation("CAA", 2), "G")
# test 9
def test_any_mutation(self):
self.assertIn(self.snv.any_mutation("CAA", 2), ["G", "C", "T"])
# test 10
def test_stoploss(self):
self.assertIn(self.snv.stoploss_mutation("TAG", 2), ["C", "T"])
# test 11
def test_stoploss_not_valid(self):
self.assertFalse(self.snv.stoploss_mutation("GGA", 2))
def test_directed_SNV_stoploss_exists(self):
snv = {
"TYPE": "SNV",
"REGION": "CODING",
"IMPACT": {
"SNV_TYPE": "STOPLOSS",
"START": 64048166
},
"ZYGOSITY": "HETEROZYGOUS"
}
snv = SNV(snv, self.negative_transcript).get_vcf_row()
self.assertEqual(snv['ref'], "C")
self.assertIn(snv['alt'], ["A", "G"])
self.assertEqual(snv['pos'], "64048166")
def test_basic_non_coding_exact(self):
snv = {
"TYPE": "SNV",
"REGION": "INTRONIC",
"IMPACT": {
"SNV_TYPE": "A",
"START": 72122000
},
"ZYGOSITY": "HETEROZYGOUS"
}
row = SNV(snv, self.positive_transcript).get_vcf_row()
self.assertEqual(row["pos"], "72122000")
self.assertEqual(row["ref"], "C")
self.assertEqual(row["alt"], "A")
def make_variant(self, var, transcript):
if var == "None":
return None
var_type = var["TYPE"]
if var_type == "SNV":
variant = SNV(var, transcript)
elif var_type == "INDEL":
variant = Indel(var, transcript)
elif var_type == "STR":
variant = ShortTandemRepeat(var, transcript)
elif var_type == "MEI":
variant = MEI(var, transcript)
elif var_type == "CLINVAR":
variant = ClinVar(var, transcript)
elif var_type == "CNV":
variant = CopyNumberVariant(var, transcript)
elif var_type == "CLINGEN":
variant = CopyNumberVariant(var, transcript)
else:
variant = Variant(var, transcript)
return variant
