计数碱基 DNA 链序列

Question

如何在 python 中编写读取 DNA 序列链的代码和 return 它是描述这三件事的重复碱基列表：哪个是碱基 (AGTC)，它在链以及重复了多少次。例如：

ACTTTTGTCTAAACCCCCGTCCTATATAATACT

这个的输出是：list_bases =[('T',3,4),('A',11,3),('C', 14,6)]

Answer 1

这是您要找的吗？

DNA_seq = 'ACTTTTGTCTAAACCCCCCGTCCTATATATAACT'
count_dic = {'A': [0,0], "G": [0,0], "C": [0,0], "T": [0,0]}
for i in range(len(DNA_seq)-1):
    j=i
    seq_count = 1
    while DNA_seq[j] == DNA_seq[j+1]:
        seq_count +=1 
        j +=1
        if seq_count > count_dic[DNA_seq[i]][1]:
            count_dic[DNA_seq[i]][1] = seq_count
            count_dic[DNA_seq[i]][0] = i + 1

count_dic的内容是

{'A': [11, 3], 'G': [0, 0], 'C': [14, 6], 'T': [3, 4]}

Answer 2

我做了以下事情：

import re
from collections import defaultdict

seq = "ACTTTTGTCTAAACCCCCCGTCCTATATATAACT"
bases = ['A','G','C','T']

indexes = defaultdict(list)
counts = dict()

for base in bases:
    comSeq = re.compile(base)
    matches = comSeq.findall(seq)
    count = len(matches)
    counts[base] = count

    start = 0

    for match in matches:
        index = seq.find(base, start)
        indexes[base].append(index)
        start = index +1

print(indexes)
print(counts)

dict 索引为您提供碱基在链中的每个位置：

{'A': [0, 10, 11, 12, 24, 26, 28, 30, 31], 'G': [6, 19], 'C': [1, 8, 13, 14,
 15, 16, 17, 18, 21, 22, 32], 'T': [2, 3, 4, 5, 7, 9, 20, 23, 25, 27, 29, 33]}

dict counts 给出了碱基在链中出现的次数：

{'A': 9, 'G': 2, 'C': 11, 'T': 12}

这可能不是最好和最有效的代码，我不确定您要的是什么，希望这对您有所帮助。

计数碱基 DNA 链序列

Counting bases DNA chain sequence

python

count

sequence