Приложение 2

from Bio import SeqIO

peaks = []
with open("H3K36me3")as f:
    for line in f:
        peaks.append(line.strip().split())

f = open('H3K36me3.bed', 'w')
for t in range(1, 25):
    if t == 23:
        t = 'X'
    if t == 24:
        t = 'Y'
    data = list(SeqIO.parse("chroms/chr" + str(t) + ".fa", "fasta"))
    length = len(data[0].seq)
    a = [0] * length
    for item in peaks:
        if item[0] == 'chr' + str(t):
            for i in range(int(item[1]) - 1, int(item[2])):
                a[i] += 1
    flag = 0
    for k in range (1, length):
        if flag == 0:
            if a[k] > a[k-1]:
                flag = 1
                start = k
        if flag == 1:
            if a[k] > a[k-1]:
                start = k
            if a[k] < a[k-1]:
                flag = 0
                f.write('chr' + str(t) + ' ' + str(start+1) + ' ' + str(k) + '\n')
f.close()