diff capture_kits.py @ 0:1a23ea467feb default tip

intial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/capture_kits.py	Thu Mar 26 09:36:17 2015 -0600
@@ -0,0 +1,29 @@
+import os
+import re
+import sys
+import operator
+import csv
+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 +  "/miseq_bam_variants.loc" ):
+    kitDir = "/export/achri_galaxy/dbs/CaptureKits/";
+else:
+    with open(kitDir + "/miseq_bam_variants.loc", "r") as tsv:
+	     for line in csv.reader(tsv, delimiter="\t"):
+		      if line[0] == 'capture_kits_dir':
+				    kitDir = line[1]
+
+def kit_fileOptions():
+    list = os.listdir(kitDir);
+    list.sort()
+    pattern = re.compile('(.*)$')
+    fileOptions = [(s) for s in list if os.path.exists(kitDir + 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
+