--- a/gops_intersect.py	Mon Apr 14 09:20:28 2014 -0400
+++ b/gops_intersect.py	Wed Nov 11 12:48:44 2015 -0500
@@ -11,34 +11,34 @@
     -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
 """
-import sys, traceback, fileinput
-from warnings import warn
-from bx.intervals import *
-from bx.intervals.io import *
-from bx.intervals.operations.intersect import *
+import fileinput
+import sys
+from bx.intervals.io import GenomicInterval, NiceReaderWrapper
+from bx.intervals.operations.intersect import intersect
 from bx.cookbook import doc_optparse
-from galaxy.tools.util.galaxyops import *
+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
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
+
 def main():
     mincols = 1
-    upstream_pad = 0
-    downstream_pad = 0
 
     options, args = doc_optparse.parse( __doc__ )
     try:
         chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
-        chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )      
-        if options.mincols: mincols = int( options.mincols )
+        chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
+        if options.mincols:
+            mincols = int( options.mincols )
         pieces = bool( options.pieces )
         in1_gff_format = bool( options.gff1 )
         in2_gff_format = bool( options.gff2 )
         in_fname, in2_fname, out_fname = args
     except:
         doc_optparse.exception()
-        
+
     # Set readers to handle either GFF or default format.
     if in1_gff_format:
         in1_reader_wrapper = GFFReaderWrapper
@@ -48,29 +48,29 @@
         in2_reader_wrapper = GFFReaderWrapper
     else:
         in2_reader_wrapper = NiceReaderWrapper
-        
+
     g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ),
-                            chrom_col=chr_col_1,
-                            start_col=start_col_1,
-                            end_col=end_col_1,
-                            strand_col=strand_col_1,
-                            fix_strand=True )
+                             chrom_col=chr_col_1,
+                             start_col=start_col_1,
+                             end_col=end_col_1,
+                             strand_col=strand_col_1,
+                             fix_strand=True )
     if in1_gff_format:
         # Intersect requires coordinates in BED format.
-        g1.convert_to_bed_coord=True
+        g1.convert_to_bed_coord = True
     g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
-                            chrom_col=chr_col_2,
-                            start_col=start_col_2,
-                            end_col=end_col_2,
-                            strand_col=strand_col_2,
-                            fix_strand=True )
+                             chrom_col=chr_col_2,
+                             start_col=start_col_2,
+                             end_col=end_col_2,
+                             strand_col=strand_col_2,
+                             fix_strand=True )
     if in2_gff_format:
         # Intersect requires coordinates in BED format.
-        g2.convert_to_bed_coord=True
-        
+        g2.convert_to_bed_coord = True
+
     out_file = open( out_fname, "w" )
     try:
-        for feature in intersect( [g1,g2], pieces=pieces, mincols=mincols ):
+        for feature in intersect( [g1, g2], pieces=pieces, mincols=mincols ):
             if isinstance( feature, GFFFeature ):
                 # Convert back to GFF coordinates since reader converted automatically.
                 convert_bed_coords_to_gff( feature )