def gotConnection(conn, authentication):
config = process_config(read_config(settings.gitosis_config))
QUEUE = random_queue()
yield conn.start(authentication)
chan = yield conn.channel(1)
yield chan.channel_open()
# Initialize the MQ state
yield chan.queue_declare(queue=QUEUE, durable=False, exclusive=False, auto_delete=True)
yield chan.exchange_declare(exchange=config['exchange'], type="fanout",
durable=True, auto_delete=False)
yield chan.queue_bind(queue=QUEUE, exchange=config['exchange'])
yield chan.basic_consume(queue=QUEUE, no_ack=True, consumer_tag="smart")
queue = yield conn.queue("smart")
recv_callback = callback_wrapper(config['projects_dir'],
config['git_user'],
config['git_server'])
yield (queue.get().addCallback(recv_callback, chan, queue))
# This is all about closing the connection nicely
yield chan.basic_cancel("smart")
yield chan.channel_close()
chan0 = yield conn.channel(0)
yield chan0.connection_close()
reactor.stop()
def gotConnection(conn, authentication, body):
config = process_config(read_config(settings.gitosis_config))
yield conn.start(authentication)
chan = yield conn.channel(1)
yield chan.channel_open()
msg = Content(body)
msg["delivery mode"] = 2
chan.basic_publish(exchange=config['exchange'], content=msg)
yield chan.channel_close()
chan0 = yield conn.channel(0)
yield chan0.connection_close()
reactor.stop()
yield chan.channel_open()
msg = Content(body)
msg["delivery mode"] = 2
chan.basic_publish(exchange=config['exchange'], content=msg)
yield chan.channel_close()
chan0 = yield conn.channel(0)
yield chan0.connection_close()
reactor.stop()
if __name__ == "__main__":
import sys
if len(sys.argv) != 3:
print "%s path_to_spec content" % sys.argv[0]
sys.exit(1)
config = process_config(read_config(settings.gitosis_config))
spec = txamqp.spec.load(sys.argv[1])
authentication = {"LOGIN": config['user_id'], "PASSWORD": config['password']}
delegate = TwistedDelegate()
d = ClientCreator(reactor, AMQClient, delegate=delegate, vhost="/",
spec=spec).connectTCP(config['host'], config['port'])
d.addCallback(gotConnection, authentication, sys.argv[2])
reactor.run()
def count_with_bedtools(gff, bam, param_dict):
count_file = bam.split(".bam")[0] + "_counts.txt"
bedtools_bin = param_dict["bin"]
strand = param_dict["strand"]
script = "{} coverage -a {} -b {} {}>{}".format(bedtools_bin, gff, bam,
strand, count_file)
return script
# def count_with_bedtools_local(gff, bam, count_file, param_dict):
#
# strand = True if param_dict["strand"] == "-s" else False
# feat = param_dict["feat"]
# a = pybedtools.BedTool(gff)
# b = pybedtools.BedTool(bam)
# counts = a.coverage(b, counts=True, s=strand)
# with open(count_file, "w") as fo:
# for f in counts.features():
# if feat not in str(f):
# continue
# else:
# identifier = str(f[-2].split("{}=".format(feat))[1].split(";")[0].strip())
# fo.write("{},{}\n".format(identifier, f[-1]))
#
# return count_file
if __name__ == "__main__":
args = get_args().parse_args()
param_dict = helpers.process_config(args.config)["bedtools"]
helpers.process_bedtools_count_output(args.input, args.output, param_dict)