count.py

import sys
import itertools as it
from collections import Counter

fn = sys.argv[1]

with open(fn) as f:
    N = sum(1 for _ in f)

counts = {}

for i in range(N):
    with open(fn) as f:
        for _ in range(i):
            next(f)
        _, A, T, G, C, x = next(f).strip().split(',')
        for j in range(i+1, N):
            _, _, _, _, _, y = next(f).strip().split(',')
            counter = Counter(zip(x,y))
            counter[('A', 'A')] += int(A)
            counter[('T', 'T')] += int(T)
            counter[('G', 'G')] += int(G)
            counter[('C', 'C')] += int(C)
            counts[(i,j)] = counter
            print("Finished processing", i, j)