Use case 2 from the DEEPBLUE Poster for the BLUEPRINT annual meeting. (09.2015). Aggregate DNA methylation signal in your own datasets by all available H3K4me3 peaks in hESCs.

deepblue-poster-01.py

# Aggregate DNA methylation signal in your own datasets by all available H3K4me3 peaks in hESCs.

import xmlrpclib
import time

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

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

(s, monocytes_biosources) = server.get_biosource_children("monocyte", user_key)
monocytes_biosources_names = [biosource[1] for biosource in monocytes_biosources]
print monocytes_biosources_names

(status, samples) = server.list_samples(monocytes_biosources_names, {"source": "BLUEPRINT Epigenome"}, user_key)
samples
samples_ids = [sample[0] for sample in samples]
(status, experiments) = server.list_experiments("", "DNA Methylation", samples_ids, "Bisulfite-Seq", "BLUEPRINT Epigenome", user_key)
print experiments


selected_experiments = []
peak_format = "CHROMOSOME,START,END,NAME,SCORE,STRAND,SIGNAL_VALUE,P_VALUE,Q_VALUE"
for experiment in experiments:
    (status, info) = server.info(experiment[0], user_key) # experiment[0] is the ID of the experiment.
    if info[0]["data_type"] == "signal" and info[0]["extra_metadata"]["FILE_TYPE"] == "BS_METH_CALL_CNAG":
        selected_experiments.append(experiment)
experiment_names = [experiment[1] for experiment in selected_experiments]
experiment_names

(status, query_id) = server.select_regions(experiment_names, None, None, None, None, None, None, None, None, user_key )

server.list_requests("", user_key)
server.get_request_data(request_id, user_key)
(status, annotation_key) = server.select_annotations("Cpg Islands", "hg19", None, None, None, user_key)

experiments_columns = {}
for experiment_name in experiment_names:
    experiments_columns[experiment_name] = "VALUE"
experiments_columns

(status, request) = server.score_matrix(experiments_columns, "mean", annotation_key , user_key )

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