diff gops_intersect.py @ 5:33b3f3688db4 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/intersect commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689

--- a/gops_intersect.py	Thu Feb 11 12:11:25 2016 -0500
+++ b/gops_intersect.py	Thu Jun 22 18:52:23 2017 -0400
@@ -11,14 +11,18 @@
     -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
     -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
 """
+from __future__ import print_function
+
 import fileinput
 import sys
+
+from bx.cookbook import doc_optparse
 from bx.intervals.io import GenomicInterval, NiceReaderWrapper
 from bx.intervals.operations.intersect import intersect
-from bx.cookbook import doc_optparse
 from bx.tabular.io import ParseError
 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
-from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff
+
+from utils.gff_util import convert_bed_coords_to_gff, GFFFeature, GFFReaderWrapper
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
@@ -80,16 +84,17 @@
                 out_file.write( "%s\n" % "\t".join( feature.fields ) )
             else:
                 out_file.write( "%s\n" % feature )
-    except ParseError, e:
+    except ParseError as e:
         out_file.close()
         fail( "Invalid file format: %s" % str( e ) )
 
     out_file.close()
 
     if g1.skipped > 0:
-        print skipped( g1, filedesc=" of 1st dataset" )
+        print(skipped( g1, filedesc=" of 1st dataset" ))
     if g2.skipped > 0:
-        print skipped( g2, filedesc=" of 2nd dataset" )
+        print(skipped( g2, filedesc=" of 2nd dataset" ))
+
 
 if __name__ == "__main__":
     main()