def EXAC(self):
if 'EXAC' in self.__dict__:
self.__dict__['EXAC']['total_homs']=self.__dict__['EXAC']['AC_Hom']/2
return
if 'EXAC_freq' in self.__dict__: return self.__dict__['EXAC_freq']
print('EXAC')
self.__dict__['EXAC_freq']=rest.exac_anno(self.data['variant_id'],update=False)
if len(self.__dict__['EXAC_freq'])>0:
self.__dict__['in_exac']=True
else:
self.__dict__['in_exac']=False
#print(self.save())
return self.__dict__['EXAC_freq']
def get_rare_var_p_hpo(gene_id, db, patient_db):
#return {'hom_comp':{p_id1:{hpo: [(HP:1234,hell)], exac_af:[0.0021], uclex_af:[0.001]},
# 'het':{p_id2: {hpo:[(HP:2345,yeah)], exac_af:[0.001,0.002],uclex_af:[0.002,0.001]}}
# sometimes variant is not in vcf. move it to debug/bad_variants for inspection and later clean
bad_var_file = open('views/debug/bad_variants', 'w')
# get all variants on this gene
all_vars = db.genes.find_one({'gene_id':gene_id})['variant_ids']
results = {'hom_comp':{}, 'het':{}}
for v in all_vars:
var = db.variants.find_one({'variant_id':v})
exac_af = 0
if var['in_exac']:
if 'allele_freq' not in var['EXAC']:
VAR = annotation.exac_anno(v)
exac_af = VAR['allele_freq']
else:
exac_af = var['EXAC']['allele_freq']
# not interested if af is > 0.01
if float(exac_af) > 0.01:
continue
# get relevant info from vcf
this = vcf_query(variant_str=v)
if not this:
bad_var_file.write(v+'\n')
continue
uclex_af = this['allele_freq']
# dealing with hom patients. also add it to het. count hom as twice
# will need to deal with both_het !!! their af are different!!!
hom_p = this['hom_samples']
for p in hom_p:
populate_mode_p(results, 2, ['hom_comp', 'het'], p, exac_af, uclex_af, patient_db)
# dealing with het patients. note to check length of exac_af. longer than one?
# also added it to 'hom_comp'
het = this['het_samples']
for p in het:
results['het'][p] = results['het'].get(p, {'exac_af':[], 'uclex_af':[]})
modes = ['het']
if results['het'][p]['exac_af']:
# this patient has more than one var on this gene. copy it to hom_comp
modes.append('hom_comp')
populate_mode_p(results, 1, modes, p, exac_af, uclex_af, patient_db)
return results
def ExAC_freq(self):
if 'ExAC_freq' in self.__dict__ and 'total_homs' in self.__dict__['ExAC_freq']: return self.__dict__['ExAC_freq']
self.__dict__['ExAC_freq']=rest.exac_anno(self.variant_id,update=False)
print(self.__dict__['ExAC_freq'].keys())
#print(self.save())
return self.__dict__['ExAC_freq']
def ExAC_freq(self):
if 'ExAC_freq' in self.__dict__ and 'total_homs' in self.__dict__['ExAC_freq']: return self.__dict__['ExAC_freq']
self.__dict__['ExAC_freq']=rest.exac_anno(self.variant_id,update=False)
print(self.__dict__['ExAC_freq'].keys())
#print(self.save())
return self.__dict__['ExAC_freq']
