erange version 4.0a dev release

[erange.git] / chkSNPrmask.py

diff --git a/chkSNPrmask.py b/chkSNPrmask.py
index 498ef491ca6e1ffda95da172e5c8a7096f75b6d5..d52c9405afa32654e0b02e4dcce0c8d5c3b1d503 100755 (executable)
--- a/chkSNPrmask.py
+++ b/chkSNPrmask.py
@@ -4,18 +4,19 @@ try:
 except:
     pass
 
-import sqlite3 as sqlite
 import sys
-import tempfile, shutil, os, optparse
-from os import environ
+import tempfile
+import shutil
+import os
+import optparse
+import sqlite3 as sqlite
+from commoncode import getConfigParser, getConfigOption, getConfigBoolOption
 
-if environ.get("CISTEMATIC_TEMP"):
-    cisTemp = environ.get("CISTEMATIC_TEMP")
-else:
-    cisTemp = "/tmp"
+configParser = getConfigParser()
+cisTemp = getConfigOption(configParser, "general", "cistematic_temp", default="/tmp")
 tempfile.tempdir = cisTemp
 
-print "version 3.3: %prog"
+print "chkSNPrmask: version 3.4"
 
 
 def main(argv=None):
@@ -24,10 +25,7 @@ def main(argv=None):
 
     usage = "usage: python %s dbfile snpsfile nr_snps_outfile [--cache numPages] [--repeats]"
 
-    parser = optparse.OptionParser(usage=usage)
-    parser.add_option("--repeats", action="store_true", dest="repeats")
-    parser.add_option("--cache", type="int", dest="cachePages")
-    parser.set_defaults(repeats=False, cachePages=None)
+    parser = makeParser(usage)
     (options, args) = parser.parse_args(argv[1:])
 
     if len(args) < 3:
@@ -41,6 +39,21 @@ def main(argv=None):
     chkSNPrmask(dbfile, filename, outfile, options.repeats, options.cachePages)
 
 
+def makeParser(usage=""):
+    parser = optparse.OptionParser(usage=usage)
+    parser.add_option("--repeats", action="store_true", dest="repeats")
+    parser.add_option("--cache", type="int", dest="cachePages")
+
+    configParser = getConfigParser()
+    section = "checkSNPrmask"
+    repeats = getConfigBoolOption(configParser, section, "repeats", False)
+    cachePages = getConfigOption(configParser, section, "cachePages", None)
+
+    parser.set_defaults(repeats=repeats, cachePages=cachePages)
+
+    return parser
+
+
 def chkSNPrmask(dbfile, filename, outfile, repeats=False, cachePages=None):
     print dbfile