python 聚合9个实验的甲基化水平

Posted 2021-05-09

import xmlrpclib
import time

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

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

experiments = ["GC_T14_10.CPG_methylation_calls.bs_call.GRCh38.20160531.wig", "C003N351.CPG_methylation_calls.bs_call.GRCh38.20160531.wig", "C005VG51.CPG_methylation_calls.bs_call.GRCh38.20160531.wig", "S002R551.CPG_methylation_calls.bs_call.GRCh38.20160531.wig", "NBC_NC11_41.CPG_methylation_calls.bs_call.GRCh38.20160531.wig", "bmPCs-V156.CPG_methylation_calls.bs_call.GRCh38.20160531.wig", "S00BS451.CPG_methylation_calls.bs_call.GRCh38.20160531.wig", "S00D1DA1.CPG_methylation_calls.bs_call.GRCh38.20160531.wig", "S00D39A1.CPG_methylation_calls.bs_call.GRCh38.20160531.wig"]

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

(status, cpgs) = server.select_annotations("Cpg Islands", "hg19", None, None, None, user_key)

(status, request_id) = server.score_matrix(experiments_columns, "mean", cpgs , user_key )

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

print score_matrix