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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
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):
def main(argv=None):
@@
-95,11
+96,9
@@
def annotateSNPFromDB(snpLocationList, snpDict, dbFileName, cachePages=None):
def annotateSNPFromDBList(snpLocationList, snpDict, dbList, 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:
tempfile.tempdir = cisTemp
for dbFileName in dbList: