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Doing operating system tasks in Python

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Doing operating system tasks in Python
1
Hans Petter Langtangen1,2
1Center for Biomedical Computing, Simula Research Laboratory 2Department of Informatics, University of Oslo
Mar 23, 2015 Python has extensive support for operating system tasks, such as file and folder management. The great advantage of doing operating system tasks in Python and not directly in the operating system is that the Python code works uniformly on Unix/Linux, Windows, and Mac (there are exceptions, but they are few). Below we list some useful operations that can be done inside a Python program or in an interactive session.
Contents
0.1 Make a folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 0.2 Make intermediate folders . . . . . . . . . . . . . . . . . . . . . . 2 0.3 Move to a folder . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 0.4 Rename a file or folder . . . . . . . . . . . . . . . . . . . . . . . . 2 0.5 List files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 0.6 List all files and folders in a folder . . . . . . . . . . . . . . . . . 3 0.7 Check if a file or folder exists . . . . . . . . . . . . . . . . . . . . 3 0.8 Remove files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 0.9 Remove a folder and all its subfolders . . . . . . . . . . . . . . . 3 0.10 Copy a file to another file or folder . . . . . . . . . . . . . . . . . 4 0.11 Copy a folder and all its subfolders . . . . . . . . . . . . . . . . . 4 0.12 Run any operating system command . . . . . . . . . . . . . . . . 4 0.13 Split file or folder name . . . . . . . . . . . . . . . . . . . . . . . 5
1The material in this document is taken from a chapter in the book A Primer on Scientific
Programming with Python, 4th edition, by the same author, published by Springer, 2014.

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0.1 Make a folder
Python applies the term directory instead of folder. The equivalent of the Unix mkdir mydir is
import os os.mkdir(��mydir��)
Ordinary files are created by the open and close functions in Python.
0.2 Make intermediate folders
Suppose you want to make a subfolder under your home folder:
$HOME/python/project1/temp
but the intermediate folders python and project1 do not exist. This requires each new folder to be made separately by os.mkdir, or you can make all folders at once with os.makedirs:
foldername = os.path.join(os.environ[��HOME��], ��python��, ��project1��, ��temp��) os.makedirs(foldername)
With os.environ[var] we can get the value of any environment variable var as a string. The os.path.join function joins folder names and a filename in a platform-independent way.
0.3 Move to a folder
The cd command reads os.chdir and cwd is os.getcwd:
origfolder = os.getcwd() # get name of current folder os.chdir(foldername) # move ("change directory") ... os.chdir(origfolder) # move back
0.4 Rename a file or folder
The cross-platform mv command is
os.rename(oldname, newname)
0.5 List files
Unix wildcard notation can be used to list files. The equivalent of ls *.py and ls plot*[1-4]*.dat reads 2

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import glob filelist1 = glob.glob(��*.py��) filelist2 = glob.glob(��plot*[1-4]*.dat��)
0.6 List all files and folders in a folder
The counterparts to ls -a mydir and just ls -a are
filelist1 = os.listdir(��mydir��) filelist1 = os.listdir(os.curdir) # current folder (directory) filelist1.sort() # sort alphabetically
0.7 Check if a file or folder exists
The widely used constructions in Unix scripts for testing if a file or folder exist are if [ -f $filename ]; then and if [ -d $dirname ]; then. These have very readable counterparts in Python:
if os.path.isfile(filename): inputfile = open(filename, ��r��) ... if os.path.isdir(dirnamename): filelist = os.listdir(dirname) ...
0.8 Remove files
Removing a single file is done with os.rename, and a loop is required for doing rm tmp_*.df:
import glob filelist = glob.glob(��tmp_*.pdf��) for filename in filelist: os.remove(filename)
0.9 Remove a folder and all its subfolders
The rm -rf mytree command removes an entire folder tree. In Python, the cross-platform valid command becomes
import shutil shutil.rmtree(foldername)
It goes without saying that this command must be used with great care! 3

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0.10 Copy a file to another file or folder
The cp fromfile tofile construction applies shutil.copy in Python:
shutil.copy(��fromfile��, ��tofile��)
0.11 Copy a folder and all its subfolders
The recursive copy command cp -r for folder trees is in Python expressed by shell.copytree:
shutil.copytree(sourcefolder, destination)
0.12 Run any operating system command
The simplest way of running another program from Python is to use os.system:
cmd = ��python myprog.py 21 --mass 4�� # command to be run failure = os.system(cmd) if failure: print ��Execution of "%s" failed!\n�� % cmd sys.exit(1)
The recommended way to run operating system commands is to use the subprocess module. The above command is equivalent to
import subprocess cmd = ��python myprog.py 21 --mass 4�� failure = subprocess.call(cmd, shell=True) # or failure = subprocess.call( [��python��, ��myprog.py��, ��21��, ��--mass��, ��4��])
The output of an operating system command can be stored in a string object:
try: output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT) except subprocess.CalledProcessError: print ��Execution of "%s" failed!\n�� % cmd sys.exit(1) # Process output for line in output.splitlines(): ...
The stderr argument ensures that the output string contains everything that the command cmd wrote to both standard output and standard error. The constructions above are mainly used for running stand-alone programs. Any file or folder listing or manipulation should be done by the functionality in the os and shutil modules. 4

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0.13 Split file or folder name
Given data/file1.dat as a file path relative to the home folder /users/me ($HOME/data/file1.dat in Unix). Python has tools for extracting the complete folder name /users/me/data, the basename file1.dat, and the extension .dat:
>>> path = os.path.join(os.environ[��HOME��], ��data��, ��file1.dat��) >>> path ��/users/me/data/file1.dat�� >>> foldername, basename = os.path.split(path) >>> foldername ��/users/me/data�� >>> basename ��file1.dat�� >>> stem, ext = os.path.splitext(basename) >>> stem ��file1�� >>> ext ��.dat�� >>> outfile = stem + ��.out�� >>> outfile ��file1.out��
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Index
check file/folder existence (in Python), 2 commands module, 3 copy files (in Python), 3 copy folders (in Python), 3 delete files (in Python), 3 delete folders (in Python), 3 directory, 1 environment variables, 1 execute programs (from Python), 3 glob.glob function, 2 list files (in Python), 2 make a folder (in Python), 1 move to a folder (in Python), 2 os module, 1 os.chdir function, 2 os.listdir function, 2 os.makedirs function, 1 os.mkdir function, 1 os.path.isdir function, 2 os.path.isfile function, 2 os.path.join function, 1 os.path.split function, 4 os.remove function, 3 os.rename function, 2 os.system function, 3 remove files (in Python), 3 remove folders (in Python), 3 rename file/folder (in Python), 2 run programs (from Python), 3 shutil.copy function, 3 shutil.copytree function, 3 shutil.rmtree function, 3 split filename, 4 subprocess module, 3 6
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