diff rest_tool.py @ 6:9ee84d9fd3a7 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool.py	Thu Apr 03 06:50:57 2014 -0400
@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+
+import sys, os
+import argparse
+
+import readfile
+
+txt_output=["cids", "aids", "sids", "synonyms" ]
+csv_output=["assaysummary"]
+check_for_id_type=["cids", "aids", "sids"]
+
+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/"
+    elif args.type == "substance":
+        url+="sid/"
+    if args.id_file is None:
+        idstring=str(args.id)
+    else:
+        idlist=readfile.getListFromFile(args.id_file)
+        idstring=",".join(idlist)
+    url+=idstring+"/"+args.operation+"/"
+    if args.operation in csv_output:
+        url+="csv"
+    elif args.operation in txt_output:
+        url+="txt"
+    else:
+        url+="xml"
+    if args.operation in check_for_id_type and not args.id_type is None:
+        url+="?"+args.operation+"_type="+args.id_type
+    print(url)
+    data=readfile.getresult(url)
+    outfile=args.outfile
+    outfile.write(data)
+    outfile.close()
+    
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--type', type=str, required=True,
+        help="That you want BioAssay Compund ...")
+    parser.add_argument('--id', type=str,
+        help="Specify the ID")
+    parser.add_argument('--operation', type=str, required=True,
+        help="Specify the operation")
+    parser.add_argument('--property-value', dest="property_value", type=str,
+        help="Specify the property")
+    parser.add_argument('--id-type', dest="id_type", type=str,
+        help="Specify the property")
+    parser.add_argument('--outfile', type=argparse.FileType('w'), required=True,
+        help="Specify one output file")
+    parser.add_argument('--id-file', dest="id_file", type=argparse.FileType('r'),
+        help="Specify a file with a list of ids, one per line")
+    if len(sys.argv) < 8:
+        print "Too few arguments..."
+        parser.print_help()
+        exit(1)
+    args = parser.parse_args()
+    main( args )