Open felipealbrecht opened 6 years ago
In [31]: import xmlrpclib ...: import time ...: ...: url = "http://deepblue.mpi-inf.mpg.de/xmlrpc" ...: user_key = "anonymous_key" ...: ...: server = xmlrpclib.Server(url, allow_none=True) ...: ...: ...: #Gene Name ...: gene_name = "RP11-34P13" ...: ...: # We obtain all versions of the gene (until version .50, is exists) ...: names = [gene_name + "." + sub for sub in [str(x) for x in range(1, 50)]] ...: ...: # Select the RP11-34P13 gene locations from gencode v23 ...: (status, q_genes) = server.select_genes(names, None, "gencode v23", None, None, None, user_key) ...: ...: # Select the genes where their 'gene_type' attribute is 'lincRNA' ...: (status, q_filter) = server.filter_regions(q_genes, "@GENE_ATTRIBUTE(gene_type)", "==", "lincRNA", "string", user_key) ...: ...: # The GTF_ATTRIBUTES column returns all attributes imported from the GTF gene. ...: (status, request_id) = server.get_regions(q_filter, "CHROMOSOME,START,END,GTF_ATTRIBUTES,@SEQUENCE", 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 ...:
111000:Unable to find the genome ''.
In [31]: import xmlrpclib ...: import time ...: ...: url = "http://deepblue.mpi-inf.mpg.de/xmlrpc" ...: user_key = "anonymous_key" ...: ...: server = xmlrpclib.Server(url, allow_none=True) ...: ...: ...: #Gene Name ...: gene_name = "RP11-34P13" ...: ...: # We obtain all versions of the gene (until version .50, is exists) ...: names = [gene_name + "." + sub for sub in [str(x) for x in range(1, 50)]] ...: ...: # Select the RP11-34P13 gene locations from gencode v23 ...: (status, q_genes) = server.select_genes(names, None, "gencode v23", None, None, None, user_key) ...: ...: # Select the genes where their 'gene_type' attribute is 'lincRNA' ...: (status, q_filter) = server.filter_regions(q_genes, "@GENE_ATTRIBUTE(gene_type)", "==", "lincRNA", "string", user_key) ...: ...: # The GTF_ATTRIBUTES column returns all attributes imported from the GTF gene. ...: (status, request_id) = server.get_regions(q_filter, "CHROMOSOME,START,END,GTF_ATTRIBUTES,@SEQUENCE", 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 ...:
111000:Unable to find the genome ''.