[SOLVED] Create regex-like (run length encoding) of string s for blocks of a given length k

Create regex-like (run length encoding) of string s for blocks of a given length k

I am looking for python code to perform a run length encoding to obtain a regex-like summary of a string s, for a known length k for the blocks. How should I tackle this?

e.g.

s=TATTTTATTTTATTTTATGTTATGTTATGTTATGTTATGTTATGTTATGTTATGTTATGTTACATTATTTTA

with k=5 could become

(TATTT)3(TATGT)9TACATTATTTTA

Solution

Instead of a regex pattern, you could split and group with itertools.groupby:

from itertools import groupby

s = "TATTTTATTTTATTTTATGTTATGTTATGTTATGTTATGTTATGTTATGTTATGTTATGTTACATTATTTTA"

k = 5
parts = [s[i:i+k] for i in range(0, len(s), k)]

for k, g in groupby(parts):
    print(k, len(list(g)))

For your specific string this would yield

TATTT 3
TATGT 9
TACAT 1
TATTT 1
TA 1

Or - if you need to stick with your specific format as well:

lst = []
for k, g in groupby(parts):
    _len = len(list(g))
    if _len > 1:
        lst.append(f"({k}){_len}")
    else:
        lst.append(k)
    

print("".join(lst))
# (TATTT)3(TATGT)9TACATTATTTTA