--- gthxmlToGFF.py	2007-06-19 11:33:42.000000000 -0500
+++ gthxmlToGFF.GFF2.py	2006-07-28 10:00:00.000000000 -0500
@@ -25,14 +25,10 @@
 '''
 
 __author__ = 'Michael E Sparks (mespar1@iastate.edu)'
-__version__ = '1.3'
-__copyright__ = 'Copyright (c) 2004, 2007 Michael E Sparks, all rights reserved'
+__version__ = '1.2'
+__copyright__ = 'Copyright (c) 2004 Michael E Sparks, all rights reserved'
 __license__ = 'BSD-style license'
 
-# MES - 19 June 2007
-# Version 1.3 updates this script to generate validating GFFv3 output:
-# http://song.sourceforge.net/gff3.shtml
-
 import getopt, sys
 from xml.sax.handler import ContentHandler
 
@@ -151,9 +147,6 @@
             self.outstream = self.outfile
         self.outstreamp = True
 
-        # Write the GFF 3 pragma
-        self.outstream.write('##gff-version 3\n')
-
         # Bools for triggering SAX events
         self.in_header = False
         self.in_splaln = False
@@ -211,8 +204,8 @@
                 self.GFF['source'] = attrs['program']
         if self.in_splaln:
             if name == 'reference':
-                self.GFF['group'] = 'transcript=' + attrs['ref_id'] + \
-                                    ';Note=' + attrs['ref_id']
+                self.GFF['group'] = 'transcript \"' + attrs['ref_id'] + \
+                                    '\" ; Note \"' + attrs['ref_id']
             if name == 'template':
                 self.GFF['template'] = attrs['temp_id']
                 self.GFF['strand'] = attrs['temp_strand']
@@ -260,7 +253,7 @@
                                  self.GFF['strand'] + '\t' + \
                                  self.GFF['phase'] + '\t' + \
                                  self.GFF['group'] + '.exon' + \
-                                 str(self.exon_ct) + '\n'
+                                 str(self.exon_ct) + '\"\n'
                 self.exon_ct += 1
                 self.exon_queue.append(self.pre_queue)
             if name == 'total_alignment_score':
@@ -306,7 +299,7 @@
                                  self.score + '\t' + \
                                  self.GFF['strand'] + '\t' + \
                                  self.GFF['phase'] + '\t' + \
-                                 self.GFF['group'] + '\n')
+                                 self.GFF['group'] + '\"\n')
             # Print the exon queue
             for x in self.exon_queue:
                 self.outstream.write(x)