|
4
|
1 #!/usr/bin/env python
|
|
|
2 # Aufruf convert_graph.py --aid list of ids --aid-from-file file
|
|
|
3
|
|
|
4 import sys, os
|
|
|
5 import networkx as nx
|
|
|
6 import argparse
|
|
|
7 import urllib2, urllib, httplib
|
|
|
8
|
|
|
9 import readfile
|
|
|
10 #supported graph_types
|
|
|
11 #output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"]
|
|
|
12
|
|
|
13
|
|
|
14 #get the cids for bioassay aid
|
|
|
15 def getCompoundList(aidlist):
|
|
|
16 aidliststring=",".join(aidlist)
|
|
|
17 url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aidliststring+"/cids/txt"
|
|
|
18 data=readfile.getresult(url)
|
|
|
19 return data
|
|
|
20
|
|
|
21 def main(args):
|
|
|
22 if args.aidfile is None:
|
|
|
23 aidlist=args.aid.split(",")
|
|
|
24 else:
|
|
|
25 aidlist=readfile.getListFromFile(args.aidfile)
|
|
|
26 cids=getCompoundList(aidlist)
|
|
|
27 args.outfile.write(cids)
|
|
|
28 args.outfile.close()
|
|
|
29
|
|
|
30
|
|
|
31 if __name__ == "__main__":
|
|
|
32 parser = argparse.ArgumentParser()
|
|
|
33 parser.add_argument('--aid', type=str,
|
|
|
34 help="AIDs of the BioAssay")
|
|
|
35 parser.add_argument('--aidfile', type=argparse.FileType('r'),
|
|
|
36 help="Specify a file with a list of aids, one per line")
|
|
|
37 parser.add_argument('--outfile', type=argparse.FileType('w'),
|
|
|
38 help="Specify output file")
|
|
|
39 if len(sys.argv) < 2:
|
|
|
40 print "Too few arguments..."
|
|
|
41 parser.print_help()
|
|
|
42 exit(1)
|
|
|
43 args = parser.parse_args()
|
|
|
44 main( args )
|
