Python: 使用循环符号将文本文件分隔为多个文件

Question

我有一个 .txt 氨基酸文件，由“>node”分隔，如下所示：

Filename.txt :

>NODE_1 MSETLVLTRPDDWHVHLRDGAALQSVVPYTARQFARAIAMPNLKPPITTAEQAQAYRERI KFFLGTDSAPHASVMKENSVCGAGCFTALSALELYAEAFEAAGALDKLEAFASFHGADFY GLPRNTTQVTLRKTEWTLPESVPFGEAAQLKPLRGGEALRWKLD*
>NODE_2 MSTWHKVQGRPKAQARRPGRKSKDDFVTRVEHDAKNDALLQLVRAEWAMLRSDIATFRGD MVERFGKVEGEITGIKGQIDGLKGEMQGVKGEVEGLRGSLTTTQWVVGTAMALLAVVTQV PSIISAYRFPPAGSSAFPAPGSLPTVPGSPASAASAP*

我想将这个文件分成两个（或尽可能多的节点）文件；

Filename1.txt :

>NODE MSETLVLTRPDDWHVHLRDGAALQSVVPYTARQFARAIAMPNLKPPITTAEQAQAYRERI KFFLGTDSAPHASVMKENSVCGAGCFTALSALELYAEAFEAAGALDKLEAFASFHGADFY GLPRNTTQVTLRKTEWTLPESVPFGEAAQLKPLRGGEALRWKLD*

Filename2.txt :

>NODE MSTWHKVQGRPKAQARRPGRKSKDDFVTRVEHDAKNDALLQLVRAEWAMLRSDIATFRGD MVERFGKVEGEITGIKGQIDGLKGEMQGVKGEVEGLRGSLTTTQWVVGTAMALLAVVTQV PSIISAYRFPPAGSSAFPAPGSLPTVPGSPASAASAP*

文件名后有数字

这段代码有效，但是它删除了“>NODE”行并且没有为最后一个节点（后面没有“>”的节点）创建文件。

with open('FilePathway') as fo:
    op = ''
    start = 0
    cntr = 1
    for x in fo.read().split("\n"):
        if x.startswith('>'):
            if start == 1:
                with open (str(cntr) + '.fasta','w') as opf:
                    opf.write(op)
                    opf.close()
                    op = ''
                    cntr += 1
            else:
                    start = 1
        else:
            if op == '':
                op = x
            else:
                op = op + '\n' + x
    fo.close()

我似乎找不到错误。如果您能指出给我，将不胜感激。

感谢您的帮助！

大家好！感谢您的所有评论。在您的帮助下，我设法让它完美地工作。对于任何有类似问题的人，这是我的最终代码：

import os
import glob

folder_path = 'FilePathway'
for filename in glob.glob(os.path.join(folder_path, '*.fasta')):
  with open(filename) as fo:
      for line in fo.readlines():
        if line.startswith('>'):
            original = line
            
content = [original]
fileno = 1
filename = filename
y = filename.replace(".fasta","_")

def writefasta():
    global content, fileno
    if len(content) > 1:
        with open(f'{y}{fileno}.fasta', 'w') as fout:
            fout.write(''.join(content))
        content = [line]
        fileno += 1


with open('FilePathway') as fin:
    for line in fin:
        if line.startswith('>NODE'):
            writefasta()
        else:
            content.append(line)
    writefasta()

Answer 1

    with open('FileName') as fo:
        cntr = 1
        for line in fo.readlines():
            with open (f'{str(cntr)}.fasta','w') as opf:
               opf.write(line)
               opf.close()
               op = ''
               cntr += 1
        fo.close()

Answer 2

这样会更好。它只会在奇数次迭代中写入。这样，“>NODE”将被跳过，文件将只为真正的内容创建。

 with open('filename.txt') as fo:
        cntr=1
        for i,content in enumerate(fo.read().split("\n")):
            if i%2 == 1:
                with open (str(cntr) + '.txt','w') as opf:
                    opf.write(content)
                    cntr += 1

顺便说一句，因为您正在使用 上下文管理器，所以您不需要关闭文件。

Context managers allow you to allocate and release resources precisely when you want to. It opens the file, writes some data to it and then closes it.

请检查：https://book.pythontips.com/en/latest/context_managers.html

Answer 3

你可以这样做：

def writefasta(d):
    if len(d['content']) > 1:
        with open(f'Filename{d["fileno"]}.fasta', 'w') as fout:
            fout.write(''.join(d['content']))
        d['content'] = ['>NODE\n']
        d['fileno'] += 1


with open('test.fasta') as fin:
    D = {'content': ['>NODE\n'], 'fileno': 1}
    for line in fin:
        if line.startswith('>NODE'):
            writefasta(D)
        else:
            D['content'].append(line)
    writefasta(D)

Python: 使用循环符号将文本文件分隔为多个文件

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