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December 17, 2015 14:38
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Output with desired columns the data from two experiments
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import xmlrpclib | |
import time | |
url = "http://deepblue.mpi-inf.mpg.de/xmlrpc" | |
user_key = "anonymous_key" | |
server = xmlrpclib.Server(url, allow_none=True) | |
# Selecting the data from 2 experiments: BL-2_c01.ERX297416.H3K27ac.bwa.GRCh38.20150527.bed and S008SGH1.ERX406923.H3K27ac.bwa.GRCh38.20150728.bed | |
# As we already know the experiments names, we keep all others fields empty. | |
# We are selecting the are in the chromosome 1, position 0 to 50.000.000. | |
(status, query_id) = server.select_experiments (["BL-2_c01.ERX297416.H3K27ac.bwa.GRCh38.20150527.bed", "S008SGH1.ERX406923.H3K27ac.bwa.GRCh38.20150728.bed"], "chr1", 0, 50000000, user_key ) | |
# Retrieve the experiments data (The @NAME meta-column is used to include the experiment name and @BIOSOURCE for experiment's biosource | |
(status, request_id) = server.get_regions(query_id, "CHROMOSOME,START,END,SIGNAL_VALUE,PEAK,@NAME,@BIOSOURCE", user_key) | |
# Wait for the server processing | |
(status, info) = server.info(request_id, user_key) | |
request_status = info[0]["state"] | |
while request_status != "done" and request_status != "failed": | |
time.sleep(1) | |
(status, info) = server.info(request_id, user_key) | |
request_status = info[0]["state"] | |
(status, regions) = server.get_request_data(request_id, user_key) | |
print regions |
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