如何使用python在DNA序列中找到连续重复？

Question

我有像

这样的DNA序列

seq='ATCGTTTTTCGAAACTGCCCCCCACTGGGGA'

我想在python中打印连续的重复核苷酸（如果它连续重复两次以上）。

对于此序列，输出应为

TTTTT
AAA
CCCCCC
GGGG

Answer 1

您可能需要查看itertools.groupby。

示例用法：

for _, group in itertools.groupby(seq):
    group = ''.join(group)
    if len(group) > 2:
        print group

Answer 2

您可以使用后引用regular expression和findall方法轻松找到重复内容;

seq = 'ATCGTTTTTCGAAACTGCCCCCCACTGGGGA'

import re
hits = re.findall(r'(([A-Z])\2\2+)', seq) # regex matching all repeating A-Z groups
print [hit[0] for hit in hits]          # Comprehension to filter the results

['TTTTT', 'AAA', 'CCCCCC', 'GGGG']

Answer 3

seq='ATCGTTTTTCGAAACTGCCCCCCACTGGGGA'
while len(seq) > 1:
    value = seq[0]
    repeats = 1
    idx = 1
    while 1:
        if seq[idx] == value:
            repeats += 1
        else:
            if repeats > 1: print value*repeats
            seq = seq[repeats:]
            break
        idx += 1