--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kmersvm/scripts/split_genome.py	Mon Aug 20 18:07:22 2012 -0400
@@ -0,0 +1,55 @@
+import os
+import os.path
+import sys
+import optparse
+import math
+import re
+from libkmersvm import *
+		
+def split(bed_file,options):
+	split_f = open(options.output, 'w')	
+	incr = options.incr
+	size = options.size
+	file = open(bed_file, 'rb')
+	
+	for line in file:		
+		(name,start,length) = line.split('\t')
+		start = int(start)
+		length = int(length)
+		end = size  + start
+
+		while True:				
+			coords = "".join([name,"\t",str(start),"\t",str(end),"\n"])
+			split_f.write(coords)
+			if end + incr >= length:
+				end += incr-((end+incr)-length)
+				start += incr	
+				coords = "".join([name,"\t",str(start),"\t",str(end),"\n"])
+				split_f.write(coords)	
+				break						
+			else:
+				start += incr
+				end += incr
+
+				
+def main(argv=sys.argv):
+	usage = "usage: %prog <bed_file>"
+	parser = optparse.OptionParser(usage=usage)
+
+	parser.add_option("-s", dest="size", type="int", \
+		default=1000, help="set chunk size")
+	parser.add_option("-i", dest="incr", type="int", \
+		default=500, help="set overlap size")
+	parser.add_option("-o", dest="output", default="split_genome_output.bed", \
+		help="output BED file (default is split_genome_output.bed)")
+		
+	(options, args) = parser.parse_args()
+        if len(args) == 0:
+		parser.print_help()
+		sys.exit(0)
+	
+	bed_file = args[0]
+	
+	split(bed_file, options)	
+
+if __name__ == "__main__": main()