diff rest_tool.py @ 2:d3f9c70919dc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool.py	Mon Mar 24 14:00:06 2014 -0400
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+# Aufruf convert_graph.py --type type --operation op --id id --outformat format --outfile outfile
+
+import sys, os
+import networkx as nx
+import argparse
+import urllib2
+
+#supported graph_types
+output_types = ["tsv", "csv", "png", "json", "txt", "xml", "sdf", "asnt", "asnb", "jsonp"]
+
+
+def getresult(url):
+    try:
+        connection = urllib2.urlopen(url)
+    except urllib2.HTTPError, e:
+        return ""
+    else:
+        return connection.read().rstrip()
+def main(args):
+    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
+    if args.type == "assay":
+        url+="aid/"
+    elif args.type == "compound":
+        url+="cid/"
+    url+=args.id+"/"+args.operation+"/"+args.outformat
+    print(url)
+    print(args.type)
+    data=getresult(url)
+    file=args.outfile
+    file.write(data)
+    file.close()
+    
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--type', type=str,
+        help="That you want BioAssay Compund ...")
+    parser.add_argument('--id', type=str,
+        help="Specify the ID")
+    parser.add_argument('--operation', type=str,
+        help="Specify the operation")
+    parser.add_argument('--property-value', type=str,
+        help="Specify the property")
+    parser.add_argument('--outformat', type=str,
+        help="Specify the format of the output", choices = output_types)
+    parser.add_argument('--outfile', type=argparse.FileType('w'),
+        help="Specify one output file")
+    if len(sys.argv) < 8:
+        print "Too few arguments..."
+        parser.print_help()
+        exit(1)
+    args = parser.parse_args()
+    main( args )