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Python script to get file path from folder to text file

import shutil
import os

def get_files():
    source = os.listdir("/output_folder/sample/cufflinks/")
    destination = "output_folder/assemblies.txt"
    for files in source:
        if files.with("transcripts.gtf"):
            shutil.move(files,destination)

I want to get transcripts.gtf

files from "/output_folder/sample/cufflinks/"

to assemblies.txt

. Whether the above code is correct or not. Please help me. Thank!

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2 answers


You can use os.walk :



import os
import shutil
from os.path import join

destination =  "/output_folder/assemblies.txt" # Absolute path, or use join
folder_to_look_in = "/output_folder/sample/cufflinks/" # Absolute folder path, or use join
for _, _, files in os.walk(folder_to_look_in):
    for file_name in files:
        if file_name.endswith("transcripts.gtf"):
            try:
                # 'a' will append the data to the tail of the file
                with open(destination, 'a') as my_super_file:
                    my_super_file.write(file_name)
            except OSError as e:
                print "I/O error({0}): {1}".format(e.errno, e.strerror)
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I think I finally understand what you are trying to achieve. Use glob.glob () function :

import glob
destination = "output_folder/assemblies.txt"
source = '/output_folder/sample/cufflinks/*/*transcripts.gtf'
with open(destination, 'w') as f:
    f.write('\n'.join(glob.glob(source))+'\n')


f.write('\n'.join(glob.glob(source))+'\n')

is equivalent to:

s = ''
for path in glob.glob(source):
    s += '{}\n'.format(path)
f.write(s)
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