3.count.py

from sys import argv
from collections import defaultdict

range_sum = 0
fns = []
for i in range(1, len(argv)):
    if i != len(argv)-1 and argv[i] == "-u":
        range_sum = int(argv[i+1])
    elif i != 0 and argv[i-1] != "-u":
        fns.append(argv[i])

bufs = defaultdict(lambda: 0)
for fn in fns:
    print ('Processing {}...'.format(fn))
    fnhead = '.'.join(fn.split('.')[:-1])
    f = open(fn)
    prev = ""
    cnt = 0
    for line in f:
        line = line.strip()
        if line != prev:
            if cnt != 0:
                pos = int(prev)
                for i in range(max(1, pos-range_sum), pos+range_sum+1):
                    bufs[i] += cnt
            prev = line
            cnt = 0
        cnt += 1
    f.close()

    pos = int(prev)
    for i in range(max(1, pos-range_sum), pos+range_sum+1):
        bufs[i] += cnt

    l = list(bufs.items())
    l.sort(key=lambda e:e[0])
    with open(fnhead + '_freq.txt', 'w') as fo:
        for key, val in l:
            fo.write("%d\t%d\n"%(key, val))