尝试创建一个循环，使用旧目录中的修改文件创建一个新目录

Question

我有一个包含 .fasta 文件的文件夹和一个 csv 文件，其中包含我需要对我的 fasta 文件夹进行的修改列表。

一个典型的fasta文件（第二行是实际数据）：

> TCTCG (this is called the header)
TAGACTGTGTCGATATGCAATAAACATATTAACTACAGGTATTCGGGTAT

csv 文件包含三列。第一列是旧目录下文件名对应的名称，第三列有新的header需要变成新的header，所以>TCTCG是替换为第三列中的项目，而 fasta 文件的第二行保持不变。

我认为最好的方法是提取 csv 文件的第一列（旧文件的名称），使用第一列中的名称遍历旧文件夹并复制所有第二列线。然后从 csv 文件的第三列复制所有新的 headers，然后创建一个新目录，并将旧文件中的第三列项目和第二行粘贴到每个新文件中（使用旧名称） .

我能够从所有旧文件中提取第二行并通读 csv 文件的第三列，但是当我尝试创建一个新目录并“写入”/“附加”新行时，什么也没有发生。我对文件 I/O 的经验很少，所以现在无法判断哪里出了问题。

import glob, os
from typing import Counter

def main():
    header_changes_knife = open('header_changes.csv','r') # the name of the csv file where the first column is the list of names of files and the third columns is the headers
    for i in header_changes_knife:
        firstColumn = [line.split(',')[0] for line in header_changes_knife] # makes a list of the first column of the header changes file, the name of the fasta file
        header_changes_knife.seek(0)
        third_column_read = [line.split(',')[2] for line in header_changes_knife] #makes a list of the third column of the header changes file, the new headers
        my_pass_to_fasta_opener = my_fasta_opener(firstColumn) # passes the first column to the function that actually reads and opens the fasta files
        for my_new_dir in header_changes_knife:
            os.chdir('C:\Users\dhaka\OneDrive\Desktop\Semester material\Data Skills class\All Homework\two\10\pauls_dna_seqs\Updated directory')
            make_new_file = open(firstColumn,"w")
            make_new_file.writelines(firstColumn)
            make_new_file.writelines(third_column_read)

def my_fasta_opener(my_list):
    counter = 0
    for my_file in my_list:
        os.chdir('C:\Users\dhaka\OneDrive\Desktop\Semester material\Data Skills class\All Homework\two\10\pauls_dna_seqs')
        file_open = open(my_list[counter])
        file_open.readline()
        second_line = file_open.readline()
        return second_line
        counter += 1

main()

Answer 1

您可以使用 built-in csv module 轻松解析 CSV 文件。在这里，我假设您在 CSV 文件中至少有两列具有各自的 header。

fasta 文件可以分为我们感兴趣的两部分：header 和 data。对于每个文件，我们根据我们的 CSV 更新 header。然后我们将更新后的数据结构存储到磁盘。

import csv

def read_csv(filename):
    """ Returns a list of rows, where each row is a dict """
    print(f'Reading csv file {filename}')
    with open(filename) as f:
        return list(csv.DictReader(f))

def read_fasta_file(filename):
    """ Returns a string tuple (header, rest_of_the_file) """
    print(f'Reading fasta file {filename}')
    with open(filename) as f:
        content = f.read()
    lines = content.spltlines()
    
    # header is the first line
    # data is the rest of the file
    header, data = lines[0], '\n'.join(lines[1:])
    return header, data


# Assumption: We have at least the columns
# target_file: The file you want to update
# new_header: The updated header
updates = read_csv('myfile.csv')

fasta_files = ['data1.fasta', 'data2.fasta']
# This is dict of the form
# {
#   'data1.fasta': ('TCTCG', '...'),
#   'data2.fasta': ('TCTCG', '...'),
# }
fasta_files = {filename: read_fasta_file(filename) for filename in fasta_files}

# Produce a new dict with the same format, but updated header values
updated_files = {}
for update in updates:
    target_filename = updates['target_file']
    old_header, data = fasta_files[target_filename]
    new_header = updates['new_header']
    updated_files[target_filename] = (new_header, data)

# Write the changes to disk
for filename, (header, data) in updated_files:
    print(f'Outputting to updated_{filename}')
    content = header + '\n' + data
    with open(f'updated_{filename}', 'w') as f:
        f.write(content)

尝试创建一个循环，使用旧目录中的修改文件创建一个新目录

Trying to make a loop that makes a new directory with modified files from an old directory

python

python-3.9