Rosalind第34题——ros_bio34_CORR

如果第一次阅读，请查看写在前面

import re


#定义一个计算hamming distance的函数
def hamm(seq1, seq2):
    dis = 0
    for i in range(len(seq1)):
        if seq1[i] == seq2[i]:
            continue
        else:
            dis += 1
    return dis


#序列的反向补码
def reverse(s):
    dic = {'A': 'T', 'G': 'C', 'C': 'G', 'T': 'A'}
    rcom = ''.join([dic[x] for x in s[::-1]])
    return rcom


#读取fasta中的序列
with open('../examples/ros_bio34_CORR.txt') as f:
    file = f.readlines()
table = {}
for line in file:
    line = re.sub(r'\n', '', line)
    m = re.match(r'^>.*', line)
    if m:
        name = m.group()
        table[name] = ''
    else:
        table[name] += line
seq = [x for x in table.values()]

#统计所有序列中的错误序列以及正确序列
correct = []
wrong = []
for i in range(len(seq)):
    remain = seq[:i] + seq[i+1:]
    length = len(correct)
    for line in remain:
        if hamm(seq[i], line) == 0 or hamm(seq[i], reverse(line)) == 0:
            correct.append(seq[i])
            break
    if len(correct) == length:
        wrong.append(seq[i])

#遍历错误序列，计算哈明距离为一的序列即为修正后的序列
result = {}
for i in wrong:
    for j in correct:
        if hamm(i, j) == 1:
            result[i] = j
        elif hamm(i, reverse(j)) == 1:
            result[i] = reverse(j)
for k, v in result.items():
    print(k, '->', v, sep='')