except:
pass
-import sys, optparse
+import sys
+import optparse
from cistematic.core import featuresIntersecting
+from commoncode import getConfigParser, getConfigOption, getConfigIntOption
-print "%prog: version 1.0"
+
+print "featureIntersects: version 1.1"
def main(argv=None):
usage = "usage: python %s tabfile [--cistype type] [--radius radius]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--cistype", action="store_false", dest="cistype")
- parser.add_option("--radius", type="int", dest="radius")
- parser.set_defaults(cistype="TFBSCONSSITES", radius=100)
+ parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 1:
featureIntersects(tabfile, options.cistype, options.radius)
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--cistype", action="store_false", dest="cistype")
+ parser.add_option("--radius", type="int", dest="radius")
+
+ configParser = getConfigParser()
+ section = "featureIntersects"
+ cistype = getConfigOption(configParser, section, "cistype", "TFBSCONSSITES")
+ radius = getConfigIntOption(configParser, section, "radius", 100)
+
+ parser.set_defaults(cistype=cistype, radius=radius)
+
+ return parser
+
+
def featureIntersects(tabFileName, cistype="TFBSCONSSITES", radius=100):
tabfile = open(tabFileName)
previous = ""