如何解决试图创建一个循环,用旧目录中的修改文件创建一个新目录
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 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 文件有三列。第一列是旧目录下文件名对应的名字,第三列有新的header需要成为新的header,所以>TCTCG
替换为第三列的一个item ,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行。然后从 csv 文件的第三列复制所有新标题,然后创建一个新目录,然后将第三列项目和旧文件中的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”/“追加”新行时,没有任何反应。我对文件 I/O 的经验很少,所以现在不知道出了什么问题。
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()
解决方法
您可以使用内置的 csv
module 轻松解析 CSV 文件。在这里,我假设您在 CSV 文件中至少有两列带有相应的标题。
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 CSV 更新标题。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)
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