#
# Created by Ali Mortazavi on 3/6/09.
#
-import sys, string, optparse
-from commoncode import writeLog
+import sys
+import string
+import optparse
+from commoncode import writeLog, getConfigParser, getConfigOption, getConfigBoolOption
-versionString = "%prog: version 1.3"
+versionString = "buildMatrix: version 1.5"
print versionString
usage = "usage: python %prog matrix.step.N-1 data.part matrix.step.N [--rescale] [--truncate maxRPKM] [--log altlogfile]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--rescale", action="store_true", dest="rescale")
- parser.add_option("--truncate", type="int", dest="maxRPKM")
- parser.add_option("--log", dest="logfilename")
- parser.set_defaults(rescale=False, maxRPKM=None, logfilename="buildMatrix.log")
+ parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 3:
options.rescale, options.logfilename)
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--rescale", action="store_true", dest="rescale")
+ parser.add_option("--truncate", type="int", dest="maxRPKM")
+ parser.add_option("--log", dest="logfilename")
+
+ configParser = getConfigParser()
+ section = "buildMatrix"
+ rescale = getConfigBoolOption(configParser, section, "rescale", False)
+ maxRPKM = getConfigOption(configParser, section, "maxRPKM", None)
+ logfilename = getConfigOption(configParser, section, "logfilename", "buildMatrix.log")
+
+ parser.set_defaults(rescale=rescale, maxRPKM=maxRPKM, logfilename=logfilename)
+
+ return parser
+
+
def buildMatrix(inFileName, colfilename, outfilename, truncateRPKM,
maxRPKM=100000000, rescale=False, logfilename="buildMatrix.log"):