test7.py

import numpy as np
import pandas as pd

file1 = "data/test.fq"
file2 = "data/test.count"
a = np.empty((0, 150))
n = 0
with open(file1) as p:
    while 1:
        d = p.readline()
        if d == "":
            break
        n += 1
        if n % 4 == 2:
            tmp = np.frombuffer(str(d[0:-1]).encode("utf-8"), dtype='S1')
            a = np.row_stack((a, tmp))

b = pd.DataFrame(a)
c = pd.DataFrame()
for v in range(150):
    tmp = b[v].value_counts()
    c = c.append(tmp)
o = c.div(c.sum(axis=1), axis=0) * 100
o.index = o.index + 1
o = o.rename(columns={b'A': 'A', b'G': 'G', b'C': 'C', b'T': 'T', b'N': 'N'})
o.to_csv(file2, sep="\t", index_label="pos")