如何在循环中使用子字符串制作字典 python

Question

我有一个包含数百万个 DNA 序列的 fasta 文件 - 对于每个 DNA 序列，还有一个 ID。

>seq1
AATCAG #----> 5mers of this line are AATCA and ATCAG
>seq3
AAATTACTACTCTCTA
>seq19
ATTACG #----> 5mers of this line are ATTAC and TTACG

我想做的是，如果 DNA 序列的长度是 6，那么我将那条线做成 5mers（如代码和上面所示）。所以我无法解决的事情是我想制作一本字典，字典显示哪个 5mers 来自哪个 sequence id.

这是我的代码，但已经进行了一半：

from Bio import SeqIO
from Bio.Seq import Seq

with open(file, 'r') as f:
    lst = []
    dict = {}
    for record in SeqIO.parse(f, 'fasta'): #reads the fast file 
        if len(record.seq) == 6:  #considers the DNA sequence length
            for i in range(len(record.seq)):
                kmer = str(record.seq[i:i + 5])
                if len(kmer) == 5:
                    lst.append(kmer)
                    dict[record.id] = kmer  #record.id picks the ids of DNA sequences


    #print(lst)
                    print(dict)

所需的词典应如下所示：

dict = {'seq1':'AATCA', 'seq1':'ATCAG', 'seq19':'ATTAC','seq19':'TTACG'}

Answer 1

按照@SulemanElahi Make a dictionary with duplicate keys in Python中的建议使用defaultdict ，因为字典中不能有重复键

from Bio import SeqIO
from collections import defaultdict

file = 'test.faa'

with open(file, 'r') as f:
    dicti = defaultdict(list)
    for record in SeqIO.parse(f, 'fasta'): #reads the fast file 
        if len(record.seq) == 6:  #considers the DNA sequence length
                kmer = str(record.seq[:5])
                kmer2 = str(record.seq[1:])
                dicti[record.id].extend((kmer,kmer2))  #record.id picks the ids of DNA sequences

print(dicti)

for i in dicti:
    for ii in dicti[i]:
        print(i, '   : ', ii)

输出：

defaultdict(<class 'list'>, {'seq1': ['AATCA', 'ATCAG'], 'seq19': ['ATTAC', 'TTACG']})
seq1    :  AATCA
seq1    :  ATCAG
seq19    :  ATTAC
seq19    :  TTACG

如何在循环中使用子字符串制作字典 python

how to make dictionary using substrings in a loop python

python

dictionary

sequence

biopython