diff rest_tool_comp_for_assay.py @ 2:d3f9c70919dc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_comp_for_assay.py	Mon Mar 24 14:00:06 2014 -0400
@@ -0,0 +1,59 @@
+#!/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
+
+#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 getresultPost(url, aidList):
+    values={'aids': ",".join(aidList)}
+    data=urllib.urlencode(values)
+    print(data)
+    
+    headers = {"Content-type": "application/x-www-form-urlencoded"}
+    conn = httplib.HTTPConnection("pubchem.ncbi.nlm.nih.gov")
+    conn.request("POST", "/rest/pug/assay/aid/aids/csv", data, headers)
+    response = conn.getresponse()
+    conn.close()
+    return response.read()
+
+
+        
+#get the cids for bioassay aid
+def getCompoundList(aid):
+    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aid+"/cids/txt"
+    data=getresult(url)
+    return data
+        
+def main(args):
+    cids=getCompoundList(args.aid)
+    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('--aid-from-file', 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 )