diff rest_tool_advanced.py @ 8:3c1e862e8cd6 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rest_tool_advanced.py	Fri May 02 05:40:28 2014 -0400
@@ -0,0 +1,80 @@
+#!/usr/bin/env python
+
+import sys, os
+import argparse
+
+import readfile
+
+#dicitionary for the output format
+
+dict_output={"cids" :"txt", "aids" : "txt", "sids" : "txt", "description": "xml", "summary" : "xml", "record" : "csv", "classification": "xml", "targets" : "txt", "xrefs" : "txt", "synonyms" : "txt", "property": "csv" }
+
+#alles andere ist xml
+check_for_id_type=["cids", "aids", "sids"]
+
+id_dict={"compound": "cid", "assay": "aid", "substance" : "sid" }
+
+def getListString(args):
+    if args.id_type_ff == "file":
+        #build comma list
+        list_string=",".join(getListFromFile(open(args.id_value,"r")))
+    else:
+        list_string=args.id_value
+    return list_string
+
+
+def main(args):
+
+    url="http://pubchem.ncbi.nlm.nih.gov/rest/pug/"+args.type+"/"
+    url+=args.id_type+"/"
+    if args.id_type ==id_dict[args.type]:
+        url+=getListString(args)+"/"
+    else:
+        url+=args.id_value+"/"
+    url+=args.operation+"/"
+    if args.operation == "target" or args.operation == "property" or args.operation == "xrefs":
+        url+=args.operation_value+"/"
+    
+    url+=dict_output[args.operation]
+    if args.operation in check_for_id_type:
+            url+="?"+args.operation+"_type="+args.ids_operation_type
+    print(url)
+    readfile.store_result(url, args.outfile)
+    
+    
+    
+    
+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', type=str,
+        help="Specify the ID type")
+    parser.add_argument('--operation', type=str, required=True,
+        help="Specify the operation")
+    parser.add_argument('--operation-value', dest="operation_value", type=str, required=False,
+        help="Specify the additional operation value")
+    parser.add_argument('--xref-operation-value', dest="xref_operation_value", type=str, required=False,
+        help="Specify the xref operation ")
+    parser.add_argument('--ids-operation-type', dest="ids_operation_type", type=str, required=False,
+        help="all inactive ...")
+    parser.add_argument('--xref', dest="xref", type=str,
+        help="use xref to identify the searched thing")
+    parser.add_argument('--xref-value', dest="xref_value", type=str,
+        help="Specify the xref")
+    parser.add_argument('--property-value', dest="property_value", type=str,
+        help="Specify the property value")
+    parser.add_argument('--id-type-ff', dest="id_type_ff", type=str,
+        help="file or field")
+    parser.add_argument('--id-value', dest="id_value", type=str, required=True,
+        help="Specify the id")
+    parser.add_argument('--outfile', type=argparse.FileType('w'), required=True,
+        help="Specify the output file")
+
+
+    if len(sys.argv) < 8:
+        print "Too few arguments..."
+        parser.print_help()
+        exit(1)
+    args = parser.parse_args()
+    main( args )