def load_mnps():
db = get_db()
start_time = time.time()
db.variants.ensure_index('has_mnp')
print 'Done indexing.'
while db.variants.find_and_modify({'has_mnp': True},
{'$unset': {
'has_mnp': '',
'mnps': ''
}}):
pass
print 'Deleted MNP data.'
with gzip.open(app.config['MNP_FILE']) as mnp_file:
for mnp in get_mnp_data(mnp_file):
variant = lookups.get_raw_variant(db, mnp['xpos'], mnp['ref'],
mnp['alt'], True)
db.variants.find_and_modify({'_id': variant['_id']}, {
'$set': {
'has_mnp': True
},
'$push': {
'mnps': mnp
}
},
w=0)
db.variants.ensure_index('has_mnp')
print 'Done loading MNP info. Took %s seconds' % int(time.time() -
start_time)
def load_mnps():
db = get_db()
start_time = time.time()
db.variants.ensure_index('has_mnp')
print 'Done indexing.'
while db.variants.find_and_modify({'has_mnp' : True}, {'$unset': {'has_mnp': '', 'mnps': ''}}):
pass
print 'Deleted MNP data.'
with gzip.open(app.config['MNP_FILE']) as mnp_file:
for mnp in get_mnp_data(mnp_file):
variant = lookups.get_raw_variant(db, mnp['xpos'], mnp['ref'], mnp['alt'], True)
db.variants.find_and_modify({'_id': variant['_id']}, {'$set': {'has_mnp': True}, '$push': {'mnps': mnp}}, w=0)
db.variants.ensure_index('has_mnp')
print 'Done loading MNP info. Took %s seconds' % int(time.time() - start_time)
def load_mnps():
db = get_db()
start_time = time.time()
db.variants.ensure_index("has_mnp")
print "Done indexing."
while db.variants.find_and_modify({"has_mnp": True}, {"$unset": {"has_mnp": "", "mnps": ""}}):
pass
print "Deleted MNP data."
with gzip.open(app.config["MNP_FILE"]) as mnp_file:
for mnp in get_mnp_data(mnp_file):
variant = lookups.get_raw_variant(db, mnp["xpos"], mnp["ref"], mnp["alt"], True)
db.variants.find_and_modify(
{"_id": variant["_id"]}, {"$set": {"has_mnp": True}, "$push": {"mnps": mnp}}, w=0
)
db.variants.ensure_index("has_mnp")
print "Done loading MNP info. Took %s seconds" % int(time.time() - start_time)