Mercurial > repos > proteore > proteore_reactome

comparison reactome_analysis.py @ 3:988a6f43acdb draft

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planemo upload commit 49c20fec48bcda2dec68fe4b26c9fb1c7554aefe-dirty
author proteore
date Tue, 11 Dec 2018 09:20:46 -0500
parents db63d069b5e6
children 34097acf457c
comparison
equal deleted inserted replaced
2:db63d069b5e6 3:988a6f43acdb
53 if header == "true": 53 if header == "true":
54 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq[1:]] 54 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq[1:]]
55 else: 55 else:
56 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq] 56 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq]
57 ids = "\n".join(id_valid(idens)[0]) 57 ids = "\n".join(id_valid(idens)[0])
58 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> /dev/null" % ids).read() 58 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1 2> stderr" % ids).read()
59 if len(id_valid(idens)[1]) > 0: 59 if len(id_valid(idens)[1]) > 0:
60 trash = id_valid(idens)[1] 60 trash = id_valid(idens)[1]
61 #print(json_string) 61 #print(json_string)
62 j = json.loads(json_string) 62 j = json.loads(json_string)
63 print ("Identifiers not found: " + str(j["identifiersNotFound"])) 63 print ("Identifiers not found: " + str(j["identifiersNotFound"]))