erange version 4.0a dev release

[erange.git] / chksnp.py

diff --git a/chksnp.py b/chksnp.py
index daf6b0adc53b871803eb5bd000f3b4f0363fc5ef..9567e5b699b1991b7208a1741442d5c80edd362a 100755 (executable)
--- a/chksnp.py
+++ b/chksnp.py
@@ -11,8 +11,9 @@ import shutil
 import os
 import string
 import sqlite3 as sqlite
+from commoncode import getConfigParser, getConfigOption
 
-print "version 3.6: %s" % sys.argv[0]
+print "chksnp: version 3.7"
 
 
 def main(argv=None):
@@ -95,11 +96,9 @@ def annotateSNPFromDB(snpLocationList, snpDict, dbFileName, cachePages=None):
 
 
 def annotateSNPFromDBList(snpLocationList, snpDict, dbList, cachePages=None):
-    if os.environ.get("CISTEMATIC_TEMP"):
-        cisTemp = os.environ.get("CISTEMATIC_TEMP")
-    else:
-        cisTemp = "/tmp"
 
+    configParser = getConfigParser()
+    cisTemp = getConfigOption(configParser, "general", "cistematic_temp", default="/tmp")
     tempfile.tempdir = cisTemp
 
     for dbFileName in dbList: