使用 Biopython 将多序列 fasta 蛋白质文件拆分为多个文件

Question

def batch_iterator(iterator, batch_size) :
    entry = True
    while entry :
        batch = []
        while len(batch) < batch_size :
            try :
                entry = iterator.__next__
            except StopIteration :
                entry = None
            if entry is None :
                #End of file
                break
            batch.append(entry)
        if batch :
            yield batch



from Bio import SeqIO

record_iter = SeqIO.parse(open("C:\Users\IDEAPAD\Desktop\fypsplit\protein.fasta"),"fasta")
for i, batch in enumerate(batch_iterator(record_iter, 1000)):
    filename = "group_%i.fasta" % (i + 1)
    with open(filename, "w") as handle:
        count = SeqIO.write(batch, handle, "fasta")
    print("Wrote %i records to %s" % (count, filename))

我正在尝试使用 Biopython 拆分一个 fasta 文件。在这个例子中我想把它变成 7 个文件。但是我在读取 AttributeError: 'function' object has no attribute 'id'.

时遇到错误

有人可以帮助我吗？提前谢谢你

Answer 1

这一行抛出了AttributeError

count = SeqIO.write(batch, handle, "fasta")

因为 SeqIO.write 需要类型 SeqRecord 的可迭代对象或列表。但是，您的 batch_iterator 生成了 方法列表 。

为什么是方法？嗯，你在这里错过了一个函数调用：

entry = iterator.__next__

应该是

entry = iterator.__next__()

这使得代码运行无误通过。

对于包含 11 个序列的测试文件，我得到了以下结果 - 在将批量大小从 1000 更改为 4 以进行测试后：

Wrote 4 records to group_1.fasta
Wrote 4 records to group_2.fasta
Wrote 3 records to group_3.fasta

Answer 2

使用可用模块：more-itertools


#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 31 08:30:32 2020

@author: Pietro

"""


from Bio import SeqIO

from more_itertools import ichunked

fasta_file = ""C:\Users\IDEAPAD\Desktop\fypsplit\protein.fasta""
seqA = record_iter = SeqIO.parse(open(fasta_file),"fasta")


group = 1

for chunk in ichunked(seqA, 1000):
    with open(fasta_file+'_group_'+str(group), "w+") as file_write:
        for seq_record in chunk:
            SeqIO.write((seq_record),file_write, "fasta")
            group += 1

使用 Biopython 将多序列 fasta 蛋白质文件拆分为多个文件

Splitting a multisequence fasta protein file into many files using Biopython

python

file

split

biopython

fasta