--- a/TEisotools-1.1.a/commons/core/coord/align2set.py	Thu Jul 21 07:36:44 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,86 +0,0 @@
-#!/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()