ratio.py

import sys
import itertools as it

stateCount = 4
transitionCount = stateCount ** 2
taxonCount = 92

f = lambda m, n, i, j: (m + n * (n - 1) // 2) * transitionCount + stateCount * i + j

for l in sys.stdin:
    D = eval(l)
    constant = sum(sum(D[f(m, n, i, i)] for i in range(stateCount)) for m, n in it.combinations(range(taxonCount), 2))
    variable = sum(sum(D[f(m, n, i, j)] + D[f(m, n, j, i)] for i, j in it.combinations(range(stateCount), 2)) for m, n in it.combinations(range(taxonCount), 2))
    print(variable/constant)

transform.py

import sys

class SR:
    pass

R = [SR() for _ in range(92)]

for i in range(92):
    l = sys.stdin.readline().strip()
    sr = R[i]
    _, sr.taxon, A, G, T, C, sr.seq = l.split(',')
    sr.A, sr.G, sr.T, sr.C = map(int, (A, G, T, C))

i = 0
for l in map(str.strip, sys.stdin):
    if l:
        sr = R[i]
        _, _, A, G, T, C, seq = l.split(',')
        sr.seq += seq
        A, G, T, C = map(int, (A, G, T, C))
        sr.A += A
        sr.G += G
        sr.T += T
        sr.C += C
        i += 1
        i %= 92

for r in R:
    print('{},{},{},{},{},{}'.format(r.taxon, r.A, r.G, r.T, r.C, r.seq))