development release: conversion of ReadDataset to use BAM files

[erange.git] / findMotifs.py

diff --git a/findMotifs.py b/findMotifs.py
index a072d43432efe3d53a9455f8e92119401049f1bd..ee2957cfdc1f5913c96fe1d75948a33c075c63d7 100755 (executable)
--- a/findMotifs.py
+++ b/findMotifs.py
@@ -54,7 +54,7 @@ def getParser(usage):
     parser.add_option("--logo", action="store_true", dest="saveLogo")
     parser.add_option("--threshold", type="float", dest="threshold")
     parser.add_option("--prefix", dest="motifPrefix")
-    parser.add_option("--numMotifs", dest="numMotifs")
+    parser.add_option("--numMotifs", type="int", dest="numMotifs")
     parser.add_option("--maxWidth", type="int", dest="maxWidth")
     parser.add_option("--maskLower", action="store_true", dest="maskLower")
 
@@ -64,7 +64,7 @@ def getParser(usage):
     doCisGreedy = getConfigBoolOption(configParser, section, "doCisGreedy", False)
     saveLogo = getConfigBoolOption(configParser, section, "saveLogo", False)
     threshold = getConfigFloatOption(configParser, section, "threshold", 75.)
-    numMotifs = getConfigOption(configParser, section, "numMotifs", "10")
+    numMotifs = getConfigOption(configParser, section, "numMotifs", 10)
     maxWidth = getConfigIntOption(configParser, section, "maxWidth", 28)
     maskLower = getConfigBoolOption(configParser, section, "maskLower", False)
 
@@ -76,7 +76,7 @@ def getParser(usage):
 
 
 def findMotifs(expbase, fsafile, doMeme=False, doCisGreedy=False, saveLogo=False, threshold=75.,
-               numMotifs="10", maxWidth=28, maskLower=False, doCisSampler=False):
+               numMotifs=10, maxWidth=28, maskLower=False, doCisSampler=False):
 
     motifPrefix = expbase