Mercurial > repos > bernhardlutz > rest_tool
comparison rest_tool.py @ 6:9ee84d9fd3a7 draft
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author | bernhardlutz |
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date | Thu, 03 Apr 2014 06:50:57 -0400 |
parents | |
children | 3c1e862e8cd6 |
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5:1ad356686717 | 6:9ee84d9fd3a7 |
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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 ) |