diff gops_concat.py @ 3:32e1c8dac438 draft

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

--- a/gops_concat.py	Wed Nov 11 12:47:51 2015 -0500
+++ b/gops_concat.py	Thu Jun 22 18:40:46 2017 -0400
@@ -12,12 +12,14 @@
     -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in second file
     -s, --sameformat: All files are precisely the same format.
 """
+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.concat import concat
-from bx.cookbook import doc_optparse
 from bx.tabular.io import ParseError
 from galaxy.tools.util.galaxyops import fail, parse_cols_arg, skipped
 
@@ -59,16 +61,17 @@
                 out_file.write( "%s\n" % "\t".join( line.fields ) )
             else:
                 out_file.write( "%s\n" % line )
-    except ParseError, exc:
+    except ParseError as exc:
         out_file.close()
         fail( "Invalid file format: %s" % str( exc ) )
 
     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()