Identification of H3k27ac peaks that overlap with promoters in all BLUEPRINT datasets and subsequent identification of transcription factor peaks that overlap with these promoters, on all ENCODE datasets

02-poster-02-overlap-tf-to-promoters-to-h3k27ac.py

import xmlrpclib
import time

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

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

(status, exps) = server.select_regions("", "GRCh38", "H3k27ac", "", "", 
                                       "BLUEPRINT Epigenome", "chr1", None,
                                        None, user_key)
(status, exps_peaks) = server.query_experiment_type(exps, "peaks", user_key)


(status, promoters) = server.select_annotations("promoters", "GRCh38","chr1", 
                                                None, None, user_key)

(status, exps_promoters) = server.intersection(exps_peaks, promoters, user_key)

(status, tf) = server.select_regions("","hg19", ["SP1"], "", 
                                     "", "ENCODE", "chr1", None, None, user_key)
(status, ts_signals) = server.query_experiment_type(tf, "signal", user_key)

(status, final) = server.intersection(tf, exps_promoters, user_key)

(status, request) = server.get_regions(final, 
                      "CHROMOSOME,START,END,@NAME,@EPIGENETIC_MARK,@BIOSOURCE",
                      user_key)

# Wait the processing
(status, info) = server.info(request, user_key)
while info[0]["state"] != "done" and info[0]["state"] != "error":
    time.sleep(5)
    print info
    (status, info) = server.info(request, user_key)

(status, regions) = server.get_request_data(request, user_key)
print regions