comparison rest_tool.py @ 6:9ee84d9fd3a7 draft

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author bernhardlutz
date Thu, 03 Apr 2014 06:50:57 -0400
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children 3c1e862e8cd6
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5:1ad356686717 6:9ee84d9fd3a7
1 #!/usr/bin/env python
2
3 import sys, os
4 import argparse
5
6 import readfile
7
8 txt_output=["cids", "aids", "sids", "synonyms" ]
9 csv_output=["assaysummary"]
10 check_for_id_type=["cids", "aids", "sids"]
11
12 def main(args):
13 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
14 if args.type == "assay":
15 url+="aid/"
16 elif args.type == "compound":
17 url+="cid/"
18 elif args.type == "substance":
19 url+="sid/"
20 if args.id_file is None:
21 idstring=str(args.id)
22 else:
23 idlist=readfile.getListFromFile(args.id_file)
24 idstring=",".join(idlist)
25 url+=idstring+"/"+args.operation+"/"
26 if args.operation in csv_output:
27 url+="csv"
28 elif args.operation in txt_output:
29 url+="txt"
30 else:
31 url+="xml"
32 if args.operation in check_for_id_type and not args.id_type is None:
33 url+="?"+args.operation+"_type="+args.id_type
34 print(url)
35 data=readfile.getresult(url)
36 outfile=args.outfile
37 outfile.write(data)
38 outfile.close()
39
40 if __name__ == "__main__":
41 parser = argparse.ArgumentParser()
42 parser.add_argument('--type', type=str, required=True,
43 help="That you want BioAssay Compund ...")
44 parser.add_argument('--id', type=str,
45 help="Specify the ID")
46 parser.add_argument('--operation', type=str, required=True,
47 help="Specify the operation")
48 parser.add_argument('--property-value', dest="property_value", type=str,
49 help="Specify the property")
50 parser.add_argument('--id-type', dest="id_type", type=str,
51 help="Specify the property")
52 parser.add_argument('--outfile', type=argparse.FileType('w'), required=True,
53 help="Specify one output file")
54 parser.add_argument('--id-file', dest="id_file", type=argparse.FileType('r'),
55 help="Specify a file with a list of ids, one per line")
56 if len(sys.argv) < 8:
57 print "Too few arguments..."
58 parser.print_help()
59 exit(1)
60 args = parser.parse_args()
61 main( args )