Aggregate genes regions

example_signal_regions.py

import xmlrpclib
import time

url = "http://deepblue.mpi-inf.mpg.de/xmlrpc"
user_key = "anonymous_key"

server = xmlrpclib.Server(url, allow_none=True)

GENOME = "hg19"
GENE_MODEL = "gencode v19"
'''
locations = """chr1	0	1000
chr1	20000	300000
chr1	40000	500000
chr1	60000	600000
chr1	80000	700000
chr1	100000	900000
chr1	120000	1300000"""

(status, regions_query_id) = server.input_regions(GENOME, locations, user_key)
'''



(status, regions_query_id) = server.select_genes(["AL672183.2", "RNU6-1205P", "ZNF692", "ZNF672"], GENE_MODEL, None, None, None, user_key)
print regions_query_id

status, chromosomes = server.chromosomes(GENOME, user_key)

# remove later
chromosomes = [chromosomes[0]]

for (chromosome_name, chromosome_size) in chromosomes:
	print chromosome_name

	(status, experiment_id) = server.select_experiments("E048-H3K4me3.fc.signal.bedgraph", chromosome_name, None, None, user_key)

	(status, aggregate_id) = server.aggregate(experiment_id, regions_query_id, "VALUE", user_key)

	FORMAT = "CHROMOSOME,START,END,@AGG.MEAN,@AGG.VAR,@AGG.COUNT"
	print FORMAT
	(status, request_id) = server.get_regions(aggregate_id, FORMAT, user_key)


	(status, info) = server.info(request_id, user_key)
	print info
	request_status = info[0]["state"]
	while request_status != "done" and request_status != "failed":
		print info
		time.sleep(1)
		(status, info) = server.info(request_id, user_key)
		request_status = info[0]["state"]

	(status, data) = server.get_request_data(request_id, user_key)
	print data