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):
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:
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