def variant_json(variant_str):
variant = orm.Variant(variant_id=variant_str, db=get_db())
if session['user'] == 'demo':
variant.__dict__['wt_samples'] = []
variant.__dict__['het_samples'] = []
variant.__dict__['hom_samples'] = []
return jsonify(result=variant.__dict__)
def common_rare_variants(individual, individual2, AC=1):
pv = []
s = subprocess.check_output([
"bgt view -s," + individual + " -s," + individual2 + " -s 'name!=\"" +
individual + "\"&&name!=\"" + individual2 +
"\"' -f 'AC1>0&&AC2>0&&AC3<%s' " % AC +
"-G /slms/gee/research/vyplab/UCLex/mainset_July2016/bgt/mainset_July2016.bgt"
],
shell=True)
#bgt view -s,IRDC_batch6_LON_2055 -s,WebsterURMD_Sample_06G02870 -s 'name!="IRDC_batch6_LON_2055"&&name!="WebsterURMD_Sample_06G02870"' -f 'AC1>0&&AC2>0&&AC3==0' -G mainset_July2016_chr1.bgt
for l in s.split('\n'):
if len(l) < 5: continue
if l.startswith('##'): continue
if l.startswith('#'):
headers = l.split('\t')
continue
d = dict(zip(headers, l.split('\t')))
d.update(dict([x.split('=') for x in d['INFO'].split(';')]))
del d['INFO']
#d['variant_id']='-'.join([d['#CHROM'],d['POS'],d['REF'],d['ALT']])
#pv.append(d)
d['variant_id'] = '-'.join([d['#CHROM'], d['POS'], d['REF'], d['ALT']])
try:
var = orm.Variant(variant_id=d['variant_id'], db=get_db())
except Exception, e:
print(e)
print(d)
continue
pv.append(var.__dict__)
def variant_page(variant_str):
try:
variant = orm.Variant(variant_id=variant_str, db=get_db())
except:
return 'Variant does not exist'
if not variant: return 'Variant does not exist'
variant = variant.__dict__
if session['user'] == 'demo':
del variant['wt_samples']
del variant['het_samples']
del variant['hom_samples']
return render_template('variant.html', title=variant_str, variant=variant)
def put_variant(variant):
"""
Add a new variant
"""
vid = variant['id'] if 'id' in variant else None
if vid is not None:
if db_session.query(orm.Variant).filter(orm.Variant.id == vid).one_or_none():
logging.info('Attempting to update existing variant %d..', vid)
return NoContent, 405
logging.info('Creating variant...')
variant['created'] = datetime.datetime.utcnow()
db_session.add(orm.Variant(**variant))
db_session.commit()
return NoContent, 201
def generate():
for l in iter(proc.stdout.readline, ''):
l = l.strip()
print(l)
if len(l) < 5: continue
if l.startswith('##'): continue
if l.startswith('#'):
headers = l.split('\t')
continue
d = dict(zip(headers, l.split('\t')))
d.update(dict([x.split('=') for x in d['INFO'].split(';')]))
del d['INFO']
if ',' in d['ALT']: d['ALT'] = d['ALT'].split(',')[0]
d['variant_id'] = '-'.join(
[d['#CHROM'], d['POS'], d['REF'], d['ALT']])
try:
var = orm.Variant(variant_id=d['variant_id'], db=get_db())
except Exception, e:
print(e)
print(d)
continue
yield flask.json.dumps(var.__dict__) + '\n'
def variant_json_db_new(variant_str):
if session['user'] == 'demo': return ''
variant = orm.Variant(variant_id=variant_str, db=get_db())
return jsonify(result=variant.__dict__)