--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/coord/align2set.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+
+import sys
+import getopt
+from commons.core.coord.Align import Align
+
+def help():
+    print
+    print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
+    print "options:"
+    print "     -h: this help"
+    print "     -i: input file name (format='align')"
+    print "     -o: output file name (format='set', default=inFileName+'.set')"
+    print "     -v: verbosity level (default=0/1)"
+    print
+    
+
+def align2set( inFileName, outFileName ):
+    alignFileHandler = open( inFileName, "r" )
+    setFileHandler = open( outFileName, "w" )
+    iAlign = Align()
+    countAlign = 0
+    while True:
+        line = alignFileHandler.readline()
+        if line == "":
+            break
+        countAlign += 1
+        iAlign.setFromString( line, "\t" )
+        setFileHandler.write( "%i\t%s\t%s\t%i\t%i\n" % ( countAlign,
+                                                         iAlign.getSubjectName(),
+                                                         iAlign.getQueryName(),
+                                                         iAlign.getQueryStart(),
+                                                         iAlign.getQueryEnd() ) )
+    alignFileHandler.close()
+    setFileHandler.close()
+
+
+def main():
+
+    inFileName = ""
+    outFileName = ""
+    verbose = 0
+
+    try:
+        opts, args = getopt.getopt( sys.argv[1:], "hi:o:v:" )
+    except getopt.GetoptError, err:
+        print str(err)
+        help()
+        sys.exit(1)
+    for o,a in opts:
+        if o == "-h":
+            help()
+            sys.exit(0)
+        elif o == "-i":
+            inFileName = a
+        elif o == "-o":
+            outFileName = a
+        elif o == "-v":
+            verbose = int(a)
+
+    if  inFileName == "":
+        print "ERROR: missing input file name"
+        help()
+        sys.exit(1)
+
+    if verbose > 0:
+        print "START %s" % ( sys.argv[0].split("/")[-1] )
+        sys.stdout.flush()
+
+    if outFileName == "":
+        outFileName = "%s.set" % ( inFileName )
+
+#TODO: move 'align2set' into 'AlignUtils.convertAlignFileIntoPSetFile' with a test
+#    AlignUtils.convertAlignFileIntoPSetFile( inFileName, outFileName )
+
+    align2set( inFileName, outFileName )
+
+    if verbose > 0:
+        print "END %s" % ( sys.argv[0].split("/")[-1] )
+        sys.stdout.flush()
+
+    return 0
+
+
+if __name__ == "__main__":
+    main()