def test_bad_formatting(self):
variant = {
"TYPE": "INDEL",
"REGION": "INTRONIC",
"CHECK": -8332,
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(KeyError):
Variant(variant, self.transcript)
def test_region_pass(self):
variant = {
"TYPE": "INDEL",
"REGION": "2:126-245",
"IMPACT": {
"INDEL_AMOUNT": -400,
"LOCATION": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
good_var = Variant(variant, self.transcript)
def test_type_fail(self):
variant = {
"TYPE": "TEST",
"REGION": "INTRONIC",
"IMPACT": {
"INDEL_AMOUNT": -400,
"LOCATION": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
Variant(variant, self.transcript)
def test_region_fail2(self):
variant = {
"TYPE": "INDEL",
"REGION": "2:126-245a",
"IMPACT": {
"INDEL_AMOUNT": -400,
"LOCATION": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
Variant(variant, self.transcript)
class VariantMethodTests(unittest.TestCase):
XKR8_uid = get_all_transcripts("XKR8", "grch38")[0]["qualifiers"]["uid"]
transcript = Transcript(XKR8_uid, "grch38")
good_var = {
"TYPE": "INDEL",
"REGION": "INTRONIC",
"IMPACT": {
"INDEL_AMOUNT": -100,
"LOCATION": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
good_var = Variant(good_var, transcript)
def test_get_type(self):
self.assertEqual(self.good_var.get_type(), "INDEL")
def test_get_region(self):
self.assertEqual(self.good_var.get_region(), "INTRONIC")
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