--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gops_join.py	Tue Apr 01 10:54:03 2014 -0400
@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+"""
+Join two sets of intervals using their overlap as the key.
+
+usage: %prog bed_file_1 bed_file_2 out_file
+    -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
+    -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
+    -m, --mincols=N: Require this much overlap (default 1bp)
+    -f, --fill=N: none, right, left, both
+"""
+import sys, traceback, fileinput
+from warnings import warn
+from bx.intervals import *
+from bx.intervals.io import *
+from bx.intervals.operations.join import *
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def main():
+    mincols = 1
+    upstream_pad = 0
+    downstream_pad = 0
+    leftfill = False
+    rightfill = False
+    
+    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 )
+        if options.fill:
+            if options.fill == "both":
+                rightfill = leftfill = True
+            else:
+                rightfill = options.fill == "right"
+                leftfill = options.fill == "left"
+        in_fname, in2_fname, out_fname = args
+    except:
+        doc_optparse.exception()
+
+    g1 = NiceReaderWrapper( 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 )
+    g2 = NiceReaderWrapper( 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 )
+
+    out_file = open( out_fname, "w" )
+
+    try:
+        for outfields in join(g1, g2, mincols=mincols, rightfill=rightfill, leftfill=leftfill):
+            if type( outfields ) is list:
+                out_file.write( "%s\n" % "\t".join( outfields ) )
+            else:
+                out_file.write( "%s\n" % outfields )
+    except ParseError, exc:
+        out_file.close()
+        fail( "Invalid file format: %s" % str( exc ) )
+    except MemoryError:
+        out_file.close()
+        fail( "Input datasets were too large to complete the join operation." )
+
+    out_file.close()
+
+    if g1.skipped > 0:
+        print skipped( g1, filedesc=" of 1st dataset" )
+    if g2.skipped > 0:
+        print skipped( g2, filedesc=" of 2nd dataset" )
+
+if __name__ == "__main__":
+    main()