def __init__(self, var_template: dict, transcript: Transcript):
try:
Variant.__init__(self, var_template, transcript)
self.element = self.impact["ELEMENT"]
self.pos = self.impact["START"]
self.check_mei()
# make mei
region_range = self.get_region_range()
if self.pos == "ANY": # pick any position within the ranges
self.pos = random.choice(region_range)
self.id = "_".join(["mei", str(self.pos+1), self.element])
self.ref = self.get_seq(self.transcript.chrom, self.pos, self.pos+1, self.transcript.genome)
self.alt = "<INS:MEI:"+self.element+">"
self.zygosity = var_template["ZYGOSITY"]
except Exception as e:
raise(e)
def __init__(self, var_template: dict, transcript: Transcript):
try:
Variant.__init__(self, var_template, transcript)
self.chrom = self.transcript.get_chr()
self.pos = self.impact["START"]
self.end = self.impact["END"]
self.copy_change = self.impact["COPY_CHANGE"]
self.check_cnv()
self.ref = self.get_anchor_position()
if self.copy_change < 0: # deletion
self.alt = "<DEL>"
else:
self.alt = "<DUP:TANDEM>"
self.id = "CNV_" + str(self.pos)
except Exception as e:
raise (e)
def test_bad_formatting(self):
variant = {
"TYPE": "INDEL",
"REGION": "INTRONIC",
"CHECK": -8332,
"ZYGOSITY": "HETEROZYGOUS"
}
with self.assertRaises(KeyError):
Variant(variant, self.transcript)
def __init__(self, var_template: dict, transcript: Transcript):
try:
Variant.__init__(self, var_template, transcript)
self.id = self.impact["CLINVAR_ID"]
clinvar = get_clinvar(self.transcript.get_genome(), self.id)
if clinvar != []:
self.pos = clinvar['start']
self.ref = clinvar['qualifiers']['ref']
self.alt = clinvar['qualifiers']['alt']
else: # no valid clinvar result
raise ValueError("type must be CLINVAR_ID")
if self.type != "CLINVAR": # check type
raise ValueError("type must be CLINVAR")
if (len(self.ref) > 1): # check location
self.check_location(self.pos, self.pos + len(self.ref))
elif (len(self.ref) == 1):
self.check_location(self.pos)
except Exception as e:
raise (e)
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)
def __init__(self, var_template, transcript: Transcript):
""" initialize snv variant """
try:
Variant.__init__(self, var_template, transcript)
self.snv_type = self.impact["SNV_TYPE"]
self.pos = self.impact["START"]
self.check_snv()
if self.region == "CODING":
if self.pos == "ANY":
var_dict = self.get_random_coding_SNV()
else:
var_dict = self.get_directed_coding_SNV(self.pos)
else:
var_dict = self.get_non_coding_SNV(
) # just make change to this
if var_dict == False:
raise Exception("Specified SNV cannot be made")
self.pos = var_dict["pos"]
self.ref = str(var_dict["ref"])
self.alt = str(var_dict["alt"])
except Exception as e:
raise (e)
def __init__(self, var_template, transcript: Transcript):
try:
Variant.__init__(self, var_template, transcript)
self.chrom = self.transcript.get_chr()
STR = get_str(self.transcript.get_genome(),
int(self.impact["STR_ID"]))
self.start = int(STR["start"])
self.end = int(STR["end"])
self.length = self.impact["LENGTH"]
self.motif = STR["qualifiers"]["motif"]
self.check_str()
# get deletion/insersion
if self.length > 0: # insersion
var_dict = self.get_expantion()
if self.length < 0: # deletion
var_dict = self.get_retraction()
self.pos = var_dict["pos"]
self.ref = str(var_dict["ref"])
self.alt = str(var_dict["alt"])
self.id = "_".join(["str", str(self.pos), str(self.length)])
except Exception as e:
raise (e)
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