erange version 4.0a dev release

[erange.git] / findMotifs.py

diff --git a/findMotifs.py b/findMotifs.py
index e79401bf3544d8a6bb33b1c83aebb6a6fec1f227..a072d43432efe3d53a9455f8e92119401049f1bd 100755 (executable)
--- a/findMotifs.py
+++ b/findMotifs.py
@@ -8,14 +8,17 @@ try:
 except:
     pass
 
-import sys, os, optparse
+import sys
+import os
+import optparse
 from cistematic.experiments.fasta import Fasta
 from cistematic.programs.meme import Meme
 from cistematic.programs.cisGreedy import CisGreedy
+from commoncode import getConfigParser, getConfigOption, getConfigIntOption, getConfigFloatOption, getConfigBoolOption
 #TODO: cisSampler is not supported yet!
 #from cistematic.programs.cisSampler import CisSampler
 
-print "%prog: version 3.4"
+print "findMotifs: version 3.5"
 
 def main(argv=None):
     if not argv:
@@ -23,18 +26,7 @@ def main(argv=None):
 
     usage = "usage: python %prog explabel regions.fsa [options]"
 
-    parser = optparse.OptionParser(usage=usage)
-    parser.add_option("--meme", action="store_true", dest="doMeme")
-    parser.add_option("--cisGreedy", action="store_true", dest="doCisGreedy")
-    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("--maxWidth", type="int", dest="maxWidth")
-    parser.add_option("--maskLower", action="store_true", dest="maskLower")
-    parser.set_defaults(doMeme=False, doCisGreedy=False, saveLogo=False,
-                        threshold=75., numMotifs="10", maxWidth=28, maskLower=False)
-
+    parser = getParser(usage)
     (options, args) = parser.parse_args(argv[1:])
 
     if len(args) < 2:
@@ -55,6 +47,34 @@ def main(argv=None):
                doCisSampler)
 
 
+def getParser(usage):
+    parser = optparse.OptionParser(usage=usage)
+    parser.add_option("--meme", action="store_true", dest="doMeme")
+    parser.add_option("--cisGreedy", action="store_true", dest="doCisGreedy")
+    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("--maxWidth", type="int", dest="maxWidth")
+    parser.add_option("--maskLower", action="store_true", dest="maskLower")
+
+    configParser = getConfigParser()
+    section = "findMotifs"
+    doMeme = getConfigBoolOption(configParser, section, "doMeme", False)
+    doCisGreedy = getConfigBoolOption(configParser, section, "doCisGreedy", False)
+    saveLogo = getConfigBoolOption(configParser, section, "saveLogo", False)
+    threshold = getConfigFloatOption(configParser, section, "threshold", 75.)
+    numMotifs = getConfigOption(configParser, section, "numMotifs", "10")
+    maxWidth = getConfigIntOption(configParser, section, "maxWidth", 28)
+    maskLower = getConfigBoolOption(configParser, section, "maskLower", False)
+
+
+    parser.set_defaults(doMeme=doMeme, doCisGreedy=doCisGreedy, saveLogo=saveLogo,
+                        threshold=threshold, numMotifs=numMotifs, maxWidth=maxWidth, maskLower=maskLower)
+
+    return parser
+
+
 def findMotifs(expbase, fsafile, doMeme=False, doCisGreedy=False, saveLogo=False, threshold=75.,
                numMotifs="10", maxWidth=28, maskLower=False, doCisSampler=False):