diff rest_tool_comp_for_assay.py @ 6:9ee84d9fd3a7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_comp_for_assay.py	Thu Apr 03 06:50:57 2014 -0400
@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+import sys, os
+import argparse
+import tempfile
+import readfile
+import rest_tool_functions
+
+        
+#get the cids for bioassay aid
+def get_aid_cid_dict_for_list(aidlist):
+    aidliststring=",".join(aidlist)
+    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/assay/aid/"+aidliststring+"/cids/xml"
+    xml=readfile.getresult(url)
+    tmp = tempfile.TemporaryFile() 
+    tmp.write(xml)
+    tmp.seek(0)
+    dic=rest_tool_functions.give_aid_cid_dict_from_xml(tmp)
+    tmp.close()
+    return dic
+        
+def main(args):
+    if args.aid_file is None:
+        aidlist=args.aid.split(",")
+    else:
+        aidlist=readfile.getListFromFile(args.aid_file)
+    dic=get_aid_cid_dict_for_list(aidlist)
+    rest_tool_functions.write_to_csv(dic, args.outfile)
+    
+    
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--aid', type=str,
+        help="AIDs of the BioAssay")
+    parser.add_argument('--aid-file', dest="aid_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 )