# ENRAGE
#
-import sys, optparse
+import sys
+import optparse
+from commoncode import getConfigParser, getConfigOption, getConfigBoolOption, getConfigIntOption
-print 'version 2.0'
+print "intersects: version 2.1"
def main(argv=None):
if not argv:
usage = "usage: python %prog infile1 infile2 outfile [options]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("-d", dest="delimiter")
- parser.add_option("--file3", dest="infile3")
- parser.add_option("-1", type="int", dest="matchfield1")
- parser.add_option("-2", type="int", dest="matchfield2")
- parser.add_option("-3", type="int", dest="matchfield3")
- parser.add_option("-reject1", dest="reject1file")
- parser.add_option("-trackGID", action="store_true", dest="trackGID")
- parser.set_defaults(delimiter="\t", infile3=None, matchField1=0, matchField2=0,
- matchField3=0, rejectFileName="", trackGID=False)
+ parser = getParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 3:
options.rejectFileName, options.trackGID)
+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("-d", dest="delimiter")
+ parser.add_option("--file3", dest="infile3")
+ parser.add_option("-1", type="int", dest="matchfield1")
+ parser.add_option("-2", type="int", dest="matchfield2")
+ parser.add_option("-3", type="int", dest="matchfield3")
+ parser.add_option("-reject1", dest="reject1file")
+ parser.add_option("-trackGID", action="store_true", dest="trackGID")
+
+ configParser = getConfigParser()
+ section = "geneMrnaCountsWeighted"
+ delimiter = getConfigOption(configParser, section, "delimiter", "\t")
+ infile3 = getConfigOption(configParser, section, "infile3", None)
+ matchField1 = getConfigIntOption(configParser, section, "matchField1", 0)
+ matchField2 = getConfigIntOption(configParser, section, "matchField2", 0)
+ matchField3 = getConfigIntOption(configParser, section, "matchField3", 0)
+ rejectFileName = getConfigOption(configParser, section, "rejectFileName", "\t")
+ trackGID = getConfigBoolOption(configParser, section, "trackGID", False)
+
+ parser.set_defaults(delimiter=delimiter, infile3=infile3, matchField1=matchField1, matchField2=matchField2,
+ matchField3=matchField3, rejectFileName=rejectFileName, trackGID=trackGID)
+
+ return parser
+
+
def intersects(infile1Name, infile2Name, outfileName, delimiter="\t", infile3Name=None,
matchField1=0, matchField2=0, matchField3=0, rejectFileName="", trackGID=False):