识别 2 个字符串之间的短匹配序列 [英] Identify short sequences of matches between 2 strings

问题描述

我有以下代码:

for k, (j,k) in enumerate (zip(line1_u,line2_u_rev_comp)):
    if j==k:
        Match1+=1 
    if j== 'N' or k == 'N':
        Unknown1+=1
    if j != k:
        Different1+=1

这需要 2 行(line1_u 和 line2_u_rev_comp)并逐个字符地比较它们以识别它们是否匹配，是否具有将其置于未知类别中或不同的 N.我想要的是统计这些中的每一个，以确定一行中是否有 10 个或更多字符匹配.这怎么可能?代码的解释将不胜感激.

This takes 2 lines (line1_u and line2_u_rev_comp) and compares them character by character to identify if they match, have an N which places it in the unknown category or are different. What I want is as well as tallying up each of these is to identify if 10 characters or more in a row match. How could this be done? Explanation of code would be greatly appreciated.

推荐答案

您应该查看 itertools.groupby:

from collections import defaultdict
from itertools import groupby

def class_chars(chrs):
    if 'N' in chrs:
        return 'unknown'
    elif chrs[0] == chrs[1]:
        return 'match'
    else:
        return 'not_match'

s1 = 'aaaaaaaaaaN123bbbbbbbbbbQccc'
s2 = 'aaaaaaaaaaN456bbbbbbbbbbPccc'
n = 0
consec_matches = []
chars = defaultdict(int)

for k, group in groupby(zip(s1, s2), class_chars):
    elems = len(list(group))
    chars[k] += elems
    if k == 'match':
        consec_matches.append((n, n+elems-1))
    n += elems

print chars
print consec_matches
print [x for x in consec_matches if x[1]-x[0] >= 9]

输出:

defaultdict(<type 'int'>, {'not_match': 4, 'unknown': 1, 'match': 23})
[(0, 9), (14, 23), (25, 27)]
[(0, 9), (14, 23)]

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