--- a/blastxml_to_gapped_gff3.py	Thu Feb 09 12:36:02 2017 -0500
+++ b/blastxml_to_gapped_gff3.py	Wed Mar 01 23:06:18 2017 -0500
@@ -1,12 +1,10 @@
 #!/usr/bin/perl
-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')
 
@@ -220,6 +218,7 @@
         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'
@@ -253,7 +252,7 @@
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='')
-    parser.add_argument('blastxml', type=open, help='Blast XML Output')
+    parser.add_argument('blastxml', type=file, 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')