erange version 4.0a dev release

[erange.git] / makewiggle.py

diff --git a/makewiggle.py b/makewiggle.py
index 95b0634bc2ec6bf804e955a1926866a9ceb28c5c..7440a796f73038130abb89ef593df425ac2921f6 100755 (executable)
--- a/makewiggle.py
+++ b/makewiggle.py
@@ -2,10 +2,12 @@
 #  makewiggle.py
 #  ENRAGE
 #
-import sys, optparse
-from commoncode import readDataset
+import sys
+import optparse
+import ReadDataset
+from commoncode import getConfigParser, getConfigOption, getConfigBoolOption, getConfigIntOption, getConfigFloatOption
 
-print "%prog: version 6.7"
+print "makewiggle: version 6.8"
 
 try:
     import psyco
@@ -20,6 +22,25 @@ def main(argv=None):
 
     usage = "usage: python %s name rdsfile outfilename [options]"
 
+    parser = getParser(usage)
+    (options, args) = parser.parse_args(argv[1:])
+
+    if len(args) < 3:
+        print usage
+        sys.exit(1)
+
+    name = args[0]
+    hitfilename = args[1]
+    outfilename = args[2]
+
+    makewiggle(name, hitfilename, outfilename, options.doNormalize, options.color, options.altColor,
+               options.limitChrom, options.shift, options.doSplit, options.listfilename, options.listPrefix,
+               options.group, options.startPriority, options.skipRandom, options.withMulti,
+               options.withSplices, options.doSingle, options.cachePages, options.enforceChr, options.strand,
+               options.chunk)
+
+
+def getParser(usage):
     parser = optparse.OptionParser(usage=usage)
     parser.add_option("--raw", action="store_false", dest="doNormalize")
     parser.add_option("--color", dest="color")
@@ -39,27 +60,35 @@ def main(argv=None):
     parser.add_option("--enforceChr", action="store_true", dest="enforceChr")
     parser.add_option("--stranded", dest="strand")
     parser.add_option("--maxchunk", type="int", dest="chunk")
-    parser.set_defaults(doNormalize=True, color=None, altColor="", limitChrom=None,
-                        shift=0, doSplit=False, listfilename=None, listPrefix="",
-                        group="", startPriority=0.01, skipRandom=False, withMulti=True,
-                        withSplices=False, doSingle=False, cachePages=-1, enforceChr=False,
-                        strand=None, chunk=20)
-
-    (options, args) = parser.parse_args(argv[1:])
-
-    if len(args) < 3:
-        print usage
-        sys.exit(1)
-
-    name = args[0]
-    hitfilename = args[1]
-    outfilename = args[2]
 
-    makewiggle(name, hitfilename, outfilename, options.doNormalize, options.color, options.altColor,
-               options.limitChrom, options.shift, options.doSplit, options.listfilename, options.listPrefix,
-               options.group, options.startPriority, options.skipRandom, options.withMulti,
-               options.withSplices, options.doSingle, options.cachePages, options.enforceChr, options.strand,
-               options.chunk)
+    configParser = getConfigParser()
+    section = "makewiggle"
+    doNormalize = getConfigBoolOption(configParser, section, "doNormalize", True)
+    color = getConfigOption(configParser, section, "color", None)
+    altColor = getConfigOption(configParser, section, "altColor", "")
+    limitChrom = getConfigOption(configParser, section, "limitChrom", None)
+    shift = getConfigIntOption(configParser, section, "shift", 0)
+    doSplit = getConfigBoolOption(configParser, section, "doSplit", False)
+    listfilename = getConfigOption(configParser, section, "listfilename", None)
+    listPrefix = getConfigOption(configParser, section, "listPrefix", "")
+    group = getConfigOption(configParser, section, "group", "")
+    startPriority = getConfigFloatOption(configParser, section, "startPriority", 0.01)
+    skipRandom = getConfigBoolOption(configParser, section, "skipRandom", False)
+    withMulti = getConfigBoolOption(configParser, section, "withMulti", True)
+    withSplices = getConfigBoolOption(configParser, section, "withSplices", False)
+    doSingle = getConfigBoolOption(configParser, section, "doSingle", False)
+    cachePages = getConfigIntOption(configParser, section, "cachePages", -1)
+    enforceChr = getConfigBoolOption(configParser, section, "enforceChr", False)
+    strand = getConfigOption(configParser, section, "strand", None)
+    chunk = getConfigIntOption(configParser, section, "chunk", 20)
+
+    parser.set_defaults(doNormalize=doNormalize, color=color, altColor=altColor, limitChrom=limitChrom,
+                        shift=shift, doSplit=doSplit, listfilename=listfilename, listPrefix=listPrefix,
+                        group=group, startPriority=startPriority, skipRandom=skipRandom, withMulti=withMulti,
+                        withSplices=withSplices, doSingle=doSingle, cachePages=cachePages, enforceChr=enforceChr,
+                        strand=strand, chunk=chunk)
+
+    return parser
 
 
 def makewiggle(name, hitfilename, outfilename, doNormalize=True, color=None, altColor="",
@@ -110,7 +139,7 @@ def makewiggle(name, hitfilename, outfilename, doNormalize=True, color=None, alt
         print "Will shift reads by +/- %d bp according to their sense" % shift
         name += "shift=%d" % shift
     
-    hitRDS = readDataset(hitfilename, verbose=True, cache=doCache)
+    hitRDS = ReadDataset.ReadDataset(hitfilename, verbose=True, cache=doCache)
 
     if cachePages > hitRDS.getDefaultCacheSize():
         hitRDS.setDBcache(cachePages)