--- a/blastxml_to_gapped_gff3.py	Wed Mar 01 23:50:09 2017 -0500
+++ b/blastxml_to_gapped_gff3.py	Thu Jun 08 17:31:17 2017 -0400
@@ -1,10 +1,12 @@
-#!/usr/bin/perl
+#!/usr/bin/env python
+import argparse
+import copy
+import logging
 import re
 import sys
-import copy
-import argparse
+
 from BCBio import GFF
-import logging
+
 logging.basicConfig(level=logging.INFO)
 log = logging.getLogger(name='blastxml2gff3')
 
@@ -218,7 +220,6 @@
         else:
             log.warn("Bad data: \n\t%s\n\t%s\n\t%s\n" % (query, match, subject))
 
-
         if strict_m:
             if ret == '=' or ret == 'X':
                 ret = 'M'
@@ -252,7 +253,7 @@
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='')
-    parser.add_argument('blastxml', type=file, help='Blast XML Output')
+    parser.add_argument('blastxml', type=open, help='Blast XML Output')
     parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3)
     parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature')
     parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene')