Importing and using modules

The following section will explore how to tap into the rest of the Python standard library by way of importing modules.

The os module

The os module provides functions that allow you to interact with the operating system. To begin using functions from os, you first need to import it

import os

Joining paths

os.path.join allows you to combine strings with the appropriate path separator

os.path.join('/path/to/data/', 'sub-001', 'ses-001')

This function call will return the path /path/to/data/sub-001/ses-001.

Listing a directory

os.listdir will list directory contents, similar to the ls utility from GNU coreutils

for entry in os.listdir('.'):
    print(entry)

Walking a directory

If you want to crawl over a directory and every subdirectory from the command line, you would run a command like ls -R or find. In Python, you can use os.walk

for root, dirs, files in os.walk('.'):
    for file in files:
        fullfile = os.path.join(root, file)
        print(fullfile)

Table of shell commands

Here's a quick list of commonly used Python functions and their corresponding GNU/Linux commands

Linux command	Python function
cd	os.chdir
pwd	os.getcwd
chmod	os.chmod
chown	os.chown
rm	os.remove
mv	os.rename

The shutil module

Similar to the os module, shutil contains more high-level functions for interacting with files and directories

import shutil

Copying a file

To copy a file, you should use shutil.copy2. This function accepts the source and destination files

shutil.copy2('/path/source.txt', '/path/destination.txt')

Python contains several functions for copying a file. There's copy, copyfile, and copy2. copy2 may be preferred under most circumstances since it preserves file metadata.

Copying a directory

To copy an entire directory tree, you would typically use the cp -R commnad. In Python, you can use shutil.copytree. This function accepts the source and destination directories

shutil.copytree('/path/source', '/path/destination')

Deleting a directory

To delete an entire directory from the command line, you would typically use rm -r and say a prayer. In Python, you would use shutil.rmtree. This function accepts the directory to delete

Destructive command

You will not be asked for confirmation. Use at your own risk.

shutil.rmtree('/be/careful')

from x import y

Instead of importing a module and calling a function

import os

os.listdir()

you can use a from statement to import only the function you need

from os import listdir

listdir()