Tuesday, April 03, 2007

Burrows-Wheeler transform in Python

def bwt(s):
s = s + '\0'
return ''.join([x[-1] for x in
sorted([s[i:] + s[:i] for i in range(len(s))])])

def ibwt(s):
L = [''] * len(s)
for i in range(len(s)):
L = sorted([s[i] + L[i] for i in range(len(s))])
return [x for x in L if x.endswith('\0')][0][:-1]
The Burrows-Wheeler transform [1] is an invertible mathematical transformation which tends to clump related sequences of data together; hence it is useful as a pre-pass for some compression algorithms. The BWT domain in the above code excludes the null character; to include the null character, modify the transformation to also output the row of sorted([s[i:] + s[:i]...]) on which s occurs, then in IBWT simply return this row after the for loop. The Python code above is not particularly fast.


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