import sys
import optparse
+from commoncode import getConfigParser, getConfigOption, getConfigFloatOption
-print "%prog: version 1.1"
+print "stallCategory: version 1.2"
def main(argv=None):
usage = "usage: python %prog stalledPercentFile1 stalledPercentFile2 transcriptFile [--out oufile] [--statout statoutfile] [--expression level]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--out", dest="outFileName")
- parser.add_option("--statout", dest="statOutFileName")
- parser.add_option("--expression", type="float", dest="expressionLevel")
- parser.set_defaults(outFileName=None, statOutFileName=None, expressionLevel=0.9)
+ parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 3:
stallCategory(infile1, infile2, transcriptFile, options.outFileName, options.statOutFileName, options.expressionLevel)
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--out", dest="outFileName")
+ parser.add_option("--statout", dest="statOutFileName")
+ parser.add_option("--expression", type="float", dest="expressionLevel")
+
+ configParser = getConfigParser()
+ section = "stallCategory"
+ outFileName = getConfigOption(configParser, section, "outFileName", None)
+ statOutFileName = getConfigOption(configParser, section, "statOutFileName", None)
+ expressionLevel = getConfigFloatOption(configParser, section, "expressionLevel", 0.9)
+
+ parser.set_defaults(outFileName=outFileName, statOutFileName=statOutFileName, expressionLevel=expressionLevel)
+
+ return parser
+
+
def stallCategory(inFile1Name, inFile2Name, transcriptFileName, outFileName=None, statOutFileName=None, expressionLevel=0.9):
infile1 = open(inFile1Name)