def get_clingen_clinvar_str_api(genome, transcript_uid, region=None):
if (region is None ):
response = jsonify([])
return response
transcript = Transcript(transcript_uid, genome)
res = []
if region in ["UTR", "INTRONIC", "GENIC", "CODING"]:
region_tuple = transcript.get_requested_region("GENIC")
else:
start = int(region.split(":")[1].split("-")[0])-1
end = int(region.split(":")[1].split("-")[1])
region_tuple = [(start, end)]
chrom = transcript.get_chr()
location = "overlapping"
# get full genic or custom region
if request.path.startswith("/get_str"):
res = get_strs(region_tuple[0][0]+1, region_tuple[0][1], chrom, genome, location) #add 1 to start to make 1 based for api call
elif request.path.startswith("/get_clinvar"):
res = get_clinvars(region_tuple[0][0]+1, region_tuple[0][1], chrom, genome, location) #add 1 to start to make 1 based for api call
else:
res = get_cnvs(region_tuple[0][0]+1, region_tuple[0][1], chrom, genome, location) #add 1 to start to make 1 based for api call
# cut if UTR, INTRONIC, or CODING
if region in ["UTR", "INTRONIC", "CODING"]:
subregions = transcript.get_requested_region(region)
res = extract_subregions(res, subregions, region)
response = jsonify(res)
return response
class Variants:
def __init__(self, variants_file):
"""
creates variants object which has gene, inheritance, var1, var2
"""
if type(variants_file) != dict:
f = open(variants_file)
variants_json = json.load(f)
f.close()
else:
variants_json = variants_file
try:
self.transcript = Transcript(variants_json["GENE_UID"],
variants_json["GENOME"])
self.var1 = self.make_variant(variants_json["VAR1"],
self.transcript)
self.var2 = self.make_variant(variants_json["VAR2"],
self.transcript)
self.sex = variants_json["SEX"]
self.check_sex_zygosity()
except Exception as e:
raise Exception(e)
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
def check_sex_zygosity(self):
if self.sex not in ['XX', 'XY']:
raise ValueError('SEX must be one of: XX, XY')
if self.transcript.chrom == 'chrY' and self.sex != 'XY':
raise ValueError('SEX of proband must be XY when selecting Y gene')
if self.var1.zygosity in ['HOMOZYGOUS', 'HEMIZYGOUS'
] and self.var2 != None:
raise ValueError(
'Cannot have a second variant if the first is HOMOZYGOUS or HEMIZYGOUS'
)
if self.var1.zygosity != 'HEMIZYGOUS' and self.sex == 'XY' and self.transcript.get_chr(
) in ["chrX", "chrY"]:
raise ValueError('With XY sex zygosity must be HEMIZYGOUS')
def variants_2_VCF(self):
""" turns variant template into variant, string representing vcf """
# print(self.var2)
r2 = ""
if self.var2 != None:
r2 = self.var2.get_vcf_row()
r1 = self.var1.get_vcf_row()
return (r1, r2)
def get_variant_rows(self):
vcf = self.variants_2_VCF()
return {"var1": vcf[0], "var2": vcf[1]}
