Mercurial > repos > proteore > proteore_reactome

comparison reactome_analysis.py @ 1:8200968789c1 draft

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planemo upload commit 1b95e5bc85662f10cdd6305587ccee8faf9a2354-dirty
author proteore
date Fri, 07 Dec 2018 10:43:57 -0500
parents 19d8daa1eb2e
children db63d069b5e6
comparison
equal deleted inserted replaced
0:19d8daa1eb2e 1:8200968789c1
43 trash = [] 43 trash = []
44 if identifiers[1] == "list": 44 if identifiers[1] == "list":
45 ids = "\n".join(id_valid(identifiers[0].split())[0]) 45 ids = "\n".join(id_valid(identifiers[0].split())[0])
46 #print(ids) 46 #print(ids)
47 #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids) 47 #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids)
48 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids).read() 48 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
49 if len(id_valid(identifiers[0].split())[1]) > 0: 49 if len(id_valid(identifiers[0].split())[1]) > 0:
50 trash = id_valid(identifiers[0].split())[1] 50 trash = id_valid(identifiers[0].split())[1]
51 elif identifiers[1] == "file": 51 elif identifiers[1] == "file":
52 header = identifiers[2] 52 header = identifiers[2]
53 mq = open(identifiers[0]).readlines() 53 mq = open(identifiers[0]).readlines()
57 else: 57 else:
58 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq] 58 idens = [x.split("\t")[int(identifiers[3].replace("c", ""))-1] for x in mq]
59 ids = "\n".join(id_valid(idens)[0]) 59 ids = "\n".join(id_valid(idens)[0])
60 #print(ids) 60 #print(ids)
61 #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids) 61 #print("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids)
62 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/projection/\?pageSize\=1\&page\=1" % ids).read() 62 json_string = os.popen("curl -H \"Content-Type: text/plain\" -d \"$(printf '%s')\" -X POST --url www.reactome.org/AnalysisService/identifiers/\?pageSize\=1\&page\=1" % ids).read()
63 if len(id_valid(idens)[1]) > 0: 63 if len(id_valid(idens)[1]) > 0:
64 trash = id_valid(idens)[1] 64 trash = id_valid(idens)[1]
65 print(json_string) 65 print(json_string)
66 return json_string, trash 66 return json_string, trash
67 67
68 def write_output(filename, json_string, trash_file, trash): 68 def write_output(filename, json_string, species, trash_file, trash):
69 """ 69 """
70 Replace json result in template and print to output 70 Replace json result in template and print to output
71 """ 71 """
72 template = open(os.path.join(CURRENT_DIR, "template.html")) 72 template = open(os.path.join(CURRENT_DIR, "template.html"))
73 output = open(filename, "w") 73 output = open(filename, "w")
74 try: 74 try:
75 for line in template: 75 for line in template:
76 if "{token}" in line: 76 if "{token}" in line:
77 line = line.replace("{species}", species)
77 line = line.replace("{token}", json.loads(json_string)["summary"]["token"]) 78 line = line.replace("{token}", json.loads(json_string)["summary"]["token"])
78 output.write(line) 79 output.write(line)
79 except ValueError: 80 except ValueError:
80 output.write("An error occurred due to unavailability of Reactome web service. Please return later.") 81 output.write("An error occurred due to unavailability of Reactome web service. Please return later.")
81 template.close() 82 template.close()
90 def options(): 91 def options():
91 parser = argparse.ArgumentParser() 92 parser = argparse.ArgumentParser()
92 argument = parser.add_argument("--json", nargs="+", required=True) 93 argument = parser.add_argument("--json", nargs="+", required=True)
93 argument = parser.add_argument("--output", default="output.html") 94 argument = parser.add_argument("--output", default="output.html")
94 argument = parser.add_argument("--trash", default="trash.txt") 95 argument = parser.add_argument("--trash", default="trash.txt")
96 argument = parser.add_argument("--species", default="48887")
95 args = parser.parse_args() 97 args = parser.parse_args()
96 filename = args.output 98 filename = args.output
97 json_string, trash = data_json(args.json) 99 json_string, trash = data_json(args.json)
98 write_output(filename, json_string, args.trash, trash) 100 write_output(filename, json_string, args.species, args.trash, trash)
99 101
100 if __name__ == "__main__": 102 if __name__ == "__main__":
101 options() 103 options()