diff rest_tool_comp_for_assay.py @ 4:54358dfa62c0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_comp_for_assay.py	Fri Mar 28 13:41:22 2014 -0400
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+# Aufruf convert_graph.py --aid list of ids --aid-from-file file
+
+import sys, os
+import networkx as nx
+import argparse
+import urllib2, urllib, httplib
+
+import readfile
+#supported graph_types
+#output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"]
+
+        
+#get the cids for bioassay aid
+def getCompoundList(aidlist):
+    aidliststring=",".join(aidlist)
+    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aidliststring+"/cids/txt"
+    data=readfile.getresult(url)
+    return data
+        
+def main(args):
+    if args.aidfile is None:
+        aidlist=args.aid.split(",")
+    else:
+        aidlist=readfile.getListFromFile(args.aidfile)
+    cids=getCompoundList(aidlist)
+    args.outfile.write(cids)
+    args.outfile.close()
+    
+    
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--aid', type=str,
+        help="AIDs of the BioAssay")
+    parser.add_argument('--aidfile', type=argparse.FileType('r'),
+        help="Specify a file with a list of aids, one per line")
+    parser.add_argument('--outfile', type=argparse.FileType('w'),
+        help="Specify output file")
+    if len(sys.argv) < 2:
+        print "Too few arguments..."
+        parser.print_help()
+        exit(1)
+    args = parser.parse_args()
+    main( args )