@@ -0,0 +1,836 @@
+# Takes a file in the format used by Valouev and extracts k-mers as new maps%0Aimport sys%0Aimport numpy as np%0Ak = 12 # window size                                                                                                                                                                                                                                                           %0Afor lno,line in enumerate(open(sys.argv%5B1%5D)):%0A    if lno %25 3 == 0:%0A        label = line.strip()%0A    if lno %25 3 == 1:%0A        parts = line.strip().split()%0A        enz, enzabr = parts%5B:2%5D%0A        frags =  parts%5B2:%5D%0A        windows = len(frags) - k%0A        if windows %3E= 0:%0A            for window in range(windows+1):%0A                print(label + %22-%22 + str(window))%0A                print(%22%5Ct%22.join(parts%5B:2%5D + frags%5Bwindow:window+k%5D))%0A                print()%0A

Add script for doing OPTIMA-overlap queries