def test_any_location_deletion(self):
indel = {
'TYPE': 'INDEL',
'REGION': 'CODING',
'IMPACT': {
"INDEL_AMOUNT": -5,
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
indel = Indel(indel, self.positive_transcript)
deletion = indel.get_deletion()
self.assertEqual(len(deletion["ref"]), 6)
self.assertEqual(len(deletion["alt"]), 1)
class InsersionMethodTesting(unittest.TestCase):
time.sleep(2)
indel_any = {
'TYPE': 'INDEL',
'REGION': 'INTRONIC',
'IMPACT': {
"INDEL_AMOUNT": 5,
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
indel_spec = {
'TYPE': 'INDEL',
'REGION': 'CODING',
'IMPACT': {
"INDEL_AMOUNT": 8,
"START": 129814200
},
"ZYGOSITY": "HETEROZYGOUS"
}
SOX9_uid = get_all_transcripts("SOX9", "grch38")[0]["qualifiers"]["uid"]
positive_transcript = Transcript(SOX9_uid, "grch38")
TOR1A_uid = get_all_transcripts("TOR1A", "grch38")[0]["qualifiers"]["uid"]
negative_transcript = Transcript(TOR1A_uid, "grch38")
indel_any = Indel(indel_any, positive_transcript)
indel_spec = Indel(indel_spec, negative_transcript)
# test 7
def test_check_insertion_generation(self):
self.assertEqual(len(self.indel_any.get_insertion_str(50)), 50)
# test 8
def test_get_insertion_any(self):
insertion = self.indel_any.get_insertion()
self.assertEqual(len(insertion["alt"]), 6)
# test 9
def test_get_insertion_spec(self):
insertion = self.indel_spec.get_insertion()
self.assertEqual(insertion["pos"], 129814199)
self.assertEqual(len(insertion["alt"]), 9)
# test 10
def test_get_insertion_row(self):
insertion = self.indel_spec.get_vcf_row()
self.assertEqual(insertion['chrom'], "9")
self.assertEqual(insertion['pos'], '129814200')
self.assertEqual(len(insertion['alt']), 9)
print(insertion)
def test_basic_deletion(self):
indel = {
'TYPE': 'INDEL',
'REGION': 'CODING',
'IMPACT': {
"INDEL_AMOUNT": -5,
"START": 72121500
},
"ZYGOSITY": "HETEROZYGOUS"
}
indel = Indel(indel, self.positive_transcript)
deletion = indel.get_deletion()
self.assertEqual(deletion["ref"], "TCGGGC")
self.assertEqual(deletion["alt"], "T")
self.assertEqual(deletion["pos"], 72121499)
def test_wrong_keys(self):
indel = {
"TYPE": "INDEL",
"REGION": "INTRONIC",
"check": 5,
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(KeyError):
Indel(indel, self.transcript)
def test_location_str(self):
indel = {
"TYPE": "INDEL",
"REGION": "INTRONIC",
"IMPACT": {
"INDEL_AMOUNT": 5,
"START": "four"
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
Indel(indel, self.SOX18).get_vcf_row()
def test_type_value_indel(self):
indel = {
"TYPE": "SNV",
"REGION": "INTRONIC",
"IMPACT": {
"INDEL_AMOUNT": 8332,
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
Indel(indel, self.transcript)
def test_region_value(self):
indel = {
"TYPE": "INDEL",
"REGION": "TEST",
"IMPACT": {
"INDEL_AMOUNT": 5,
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
Indel(indel, self.transcript)
def test_raises_length_over_200(self):
indel = {
'TYPE': 'INDEL',
'REGION': 'CODING',
'IMPACT': {
"INDEL_AMOUNT": 570,
"START": "ANY"
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
Indel(indel, self.positive_transcript).get_deletion()
def test_raises_length_greater_than_location(self):
SOX18_uid = get_all_transcripts("SOX18",
"grch38")[0]["qualifiers"]["uid"]
SOX18 = Transcript(SOX18_uid, "grch38")
indel = {
'TYPE': 'INDEL',
'REGION': 'INTRONIC',
'IMPACT': {
"INDEL_AMOUNT": -150,
"START": 64049150
},
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(ValueError):
indel = Indel(indel, SOX18)
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