erange 4.0a dev release with integrated cistematic

[erange.git] / rnapath / RNAPATH.py

diff --git a/rnapath/RNAPATH.py b/rnapath/RNAPATH.py
index 86f61cd761c2b42d3fd5830452008c0377960977..030e70ac0661064e6e0e449e89a695eed11c47cf 100644 (file)
--- a/rnapath/RNAPATH.py
+++ b/rnapath/RNAPATH.py
@@ -2,8 +2,9 @@ import sys
 import optparse
 import string
 from numpy import zeros, int16
+from erange.commoncode import getConfigParser, getConfigOption, getConfigIntOption
 
-versionString = "%s: version 0.95" % sys.argv[0]
+versionString = "RNAPATH: version 0.96"
 print versionString
 
 
@@ -67,10 +68,7 @@ def main(argv=None):
 
     usage = "python %prog incontigfile distalPairs outpathfile outcontigfile [--prefix string] [--overlap bp]"
 
-    parser = optparse.OptionParser(usage=usage)
-    parser.add_option("--prefix", dest="pathPrefix")
-    parser.add_option("--overlap", type="int", dest="overlap")
-    parser.set_defaults(pathPrefix="RNAPATH", overlap=30)
+    parser = getParser(usage)
     (options, args) = parser.parse_args(argv[1:])
 
     if len(args) < 4:
@@ -86,6 +84,21 @@ def main(argv=None):
             outcontigfilename, options.pathPrefix, options.overlap)
 
 
+def getParser(usage):
+    parser = optparse.OptionParser(usage=usage)
+    parser.add_option("--prefix", dest="pathPrefix")
+    parser.add_option("--overlap", type="int", dest="overlap")
+
+    configParser = getConfigParser()
+    section = "RNAPATH"
+    pathPrefix = getConfigOption(configParser, section, "pathPrefix", "RNAPATH")
+    overlap = getConfigIntOption(configParser, section, "overlap", 30)
+
+    parser.set_defaults(pathPrefix=pathPrefix, overlap=overlap)
+
+    return parser
+
+
 def rnaPath(incontigfilename, distalPairsfile, outpathfilename,
             outcontigfilename, pathPrefix="RNAPATH", overlap=30):