--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/polyphen_datasets.py	Wed Mar 25 16:00:12 2015 -0600
@@ -0,0 +1,29 @@
+import os
+import re
+import csv
+import operator
+from galaxy import config
+
+# get tool-data path
+configur =  config.Configuration()
+kitDir = configur.resolve_path("tool-data")
+
+# determine if config file exists
+if not os.path.exists( kitDir +  "/hgvs_annotate.loc" ):
+    kitDir = "/export/geno_tmp/achri/dbs/";
+else:
+	 with open(kitDir + "/hgvs_annotate.loc", "r") as tsv:
+	   for line in csv.reader(tsv, delimiter="\t"):
+		    if line[0] == 'pathways_dbs':
+			       kitDir = line[1]
+
+
+polyPhenDir = kitDir
+def PolyPhen_fileOptions():
+    list = os.listdir(polyPhenDir);
+    list.sort()
+    pattern = re.compile('polyphen_(.*)\.txt.gz$')
+    fileOptions = [(s) for s in list if os.path.exists(polyPhenDir + s)]
+    ds = [pattern.match(s) for s in fileOptions]
+    datasets = [(m.group(1), m.group(1), False) for m in ds if m]
+    return datasets