--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/windowSplitter.py	Tue Apr 01 10:50:03 2014 -0400
@@ -0,0 +1,84 @@
+#!/usr/bin/env python
+
+"""
+Split into windows.
+
+usage: %prog input size out_file
+   -l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
+"""
+
+import sys
+
+from galaxy import eggs
+import pkg_resources
+pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+from galaxy.tools.util.galaxyops import *
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+
+def main():
+    # Parsing Command Line here
+    options, args = doc_optparse.parse( __doc__ )
+    
+    try:
+        chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols )
+        inp_file, winsize, out_file, makesliding, offset = args
+        winsize = int(winsize)
+        offset = int(offset)
+        makesliding = int(makesliding)
+    except:
+        stop_err( "Data issue, click the pencil icon in the history item to correct the metadata attributes of the input dataset." )
+    
+    fo = open(out_file,'w')
+
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_line = None
+    if offset == 0:
+        makesliding = 0
+
+    for i, line in enumerate( file( inp_file ) ):
+        line = line.strip()
+        if line and line[0:1] != "#":
+            try:
+                elems = line.split('\t')
+                start = int(elems[start_col_1])
+                end = int(elems[end_col_1])
+                if makesliding == 0:
+                    numwin = (end - start)/winsize
+                else:
+                    numwin = (end - start)/offset
+                if numwin > 0:
+                    for win in range(numwin):
+                        elems_1 = elems
+                        elems_1[start_col_1] = str(start)
+                        elems_1[end_col_1] = str(start + winsize)
+                        fo.write( "%s\n" % '\t'.join( elems_1 ) )
+                        if makesliding == 0:
+                            start = start + winsize
+                        else:
+                            start = start + offset
+                            if start+winsize > end:
+                                break
+            except:
+                skipped_lines += 1
+                if not invalid_line:
+                    first_invalid_line = i + 1
+                    invalid_line = line
+    
+    fo.close()
+
+    if makesliding == 1:
+        print 'Window size=%d, Sliding=Yes, Offset=%d' % ( winsize, offset )
+    else:
+        print 'Window size=%d, Sliding=No' % (winsize)
+    if skipped_lines > 0:
+        print 'Skipped %d invalid lines starting with #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
+
+
+if __name__ == "__main__":
+    main()