def main():
args = parse_args()
DBCONN = db_connect(os.path.realpath(__file__))
run(args, DBCONN)
return 0
def main():
from dbconnect import db_connect
testCONN = db_connect(os.path.realpath(__file__))
assembly = "hg19"
#assembly = "mm10"
pw = PostgresWrapper(testCONN)
queries = ["BAP1", "HBB", "Actin alpha 1", "chr1:10-100"]
queries = ["BAP1"]
queries = ["Actin alpha 1", "HBB"]
queries = ["HBB"]
queries = ["Actin alpha 1"]
queries = ["EH37E1177528"]
for q in queries:
print("***************", q)
ps = ParseSearch(pw, assembly, {"q": q})
output = ps.parse()
keys = sorted(output.keys())
for k in keys:
v = output[k]
if "genes" == k:
for g in v:
print(g)
else:
print(k + ':', v)
def main():
import sys
import os
sys.path.append(os.path.join(os.path.dirname(__file__), ".."))
sys.path.append(os.path.join(os.path.dirname(__file__), "../common"))
sys.path.append(os.path.join(os.path.dirname(__file__), "../../common"))
from postgres_wrapper import PostgresWrapper
from pg import PGsearch
from dbconnect import db_connect
from cached_objects import CachedObjects
testCONN = db_connect(os.path.realpath(__file__))
ps = PostgresWrapper(testCONN)
# GE
for assembly in ["hg19", "mm10"]:
pgSearch = PGsearch(ps, assembly)
cache = CachedObjects(ps, assembly)
tissueToColor = cache.colors["tissues"]
for t in pgSearch.geneExpressionTissues():
if t not in tissueToColor:
print("missing", t)
# RAMPAGE
for assembly in ["hg19"]:
pgSearch = PGsearch(ps, assembly)
cache = CachedObjects(ps, assembly)
ri = pgSearch.rampage_info()
tissueToColor = cache.colors["tissues"]
for fileID, info in ri.items():
t = info["tissue"]
if t not in tissueToColor:
print("missing", t)
def main():
testCONN = db_connect(os.path.realpath(__file__))
ps = PostgresWrapper(testCONN)
cache = CachedObjects(ps, "mm10")
pgSearch = PGsearch(ps, "mm10")
n = pgSearch.datasets("DNase")
for k, v in cache.assaymap["dnase"].items():
print(k, v, n[k])
def main():
args = parse_args()
DBCONN = db_connect(os.path.realpath(__file__))
assemblies = ["hg19", "mm10"]
if args.assembly:
assemblies = [args.assembly]
for assembly in assemblies:
print('***********', assembly)
ctt = CheckCellTypes(DBCONN, assembly)
ctt.run()
return 0
def main():
from utils import Utils, eprint, AddPath
AddPath(__file__, '../../common/')
from dbconnect import db_connect
from postgres_wrapper import PostgresWrapper
AddPath(__file__, '../../website/common/')
from pg import PGsearch
from cached_objects import CachedObjects
from pg_common import PGcommon
testCONN = db_connect(os.path.realpath(__file__))
ps = PostgresWrapper(testCONN)
pgSearch = PGsearch(ps, "hg19")
ds = Datasets("hg19", pgSearch)
for ctn, vs in ds.byCellType.items():
for v in vs:
print(ctn, v)
def main():
args = parse_args()
AddPath(__file__, '../../common/')
from dbconnect import db_connect
from postgres_wrapper import PostgresWrapper
AddPath(__file__, '../../api/common/')
from pg import PGsearch
from cached_objects import CachedObjects
from pg_common import PGcommon
from db_trackhub import DbTrackhub
from cached_objects import CachedObjectsWrapper
DBCONN = db_connect(os.path.realpath(__file__))
ps = PostgresWrapper(DBCONN)
cacheW = CachedObjectsWrapper(ps)
db = DbTrackhub(DBCONN)
tdb = TrackhubDb(ps, cacheW, db, UCSC)
for assembly in ["hg19", "mm10"]:
tdb.makeAllTracks(assembly)
def main():
from dbconnect import db_connect
testCONN = db_connect(os.path.realpath(__file__))
pw = PostgresWrapper(testCONN)
for assembly in ["hg19", "mm10"]:
print("*************", assembly)
cart = PGcart(pw, assembly)
uuid = "test"
j = {"a": [1, 2, 3]}
cart.set(uuid, j)
print(cart.get(uuid))
j = {"b": [5, 6, 7]}
cart.set(uuid, j)
print(cart.get(uuid))
print(cart.get("nocart"))
j = {"b": []}
cart.set(uuid, json.dumps(j))
print(cart.get(uuid))
def main():
import sys
import os
sys.path.append(os.path.join(os.path.dirname(__file__), ".."))
sys.path.append(os.path.join(os.path.dirname(__file__), "../common"))
sys.path.append(os.path.join(os.path.dirname(__file__), "../../common"))
from postgres_wrapper import PostgresWrapper
from pg import PGsearch
from dbconnect import db_connect
from cached_objects import CachedObjects
testCONN = db_connect(os.path.realpath(__file__))
ps = PostgresWrapper(testCONN)
assembly = "GRCh38"
acc = "EH38E1516978"
pgSearch = PGsearch(ps, assembly)
cache = CachedObjects(ps, assembly)
mp = MiniPeaks(assembly, pgSearch, cache, 0, 4)
ret = mp.getMinipeaksForAssays(["dnase"], [acc])
print(ret)
def main():
args = parse_args()
if args.production:
args.dev = False
DBCONN = db_connect(os.path.realpath(__file__))
ps = PostgresWrapper(DBCONN)
cow = CachedObjectsWrapper(ps)
wsconfig = WebServerConfig("main", args.production)
main = Apis(args, wsconfig.viewDir, wsconfig.staticDir, ps, cow)
cherrypy.tree.mount(main, '/', wsconfig.getRootConfig())
cherrypy.config.update({
'server.socket_host': '0.0.0.0',
'server.socket_port': int(args.port),
'tools.encode.text_only': False
})
if args.dev:
cherrypy.config.update({
'server.environment': "development",
'server.socket_queue_size': 128,
'server.thread_pool': 8,
})
if args.production:
cherrypy.config.update({
'server.socket_queue_size': 512,
'server.thread_pool': 30,
'log.screen': False,
'log.access_file': "",
'log.error_file': wsconfig.errorFnp
})
cherrypy.engine.start()
cherrypy.engine.block()
