I would like some help to loop through some directories and subdirectories and extracting data. I have a directory with three levels, with the third level containing several .csv.gz files. The structure is like this
I need to access level 2 (where subfolders are) of each folder and check the existence of a specific folder (in my example, this will be subfolder 3; I left the other folders empty for this example, but in real cases they will have data). If checking returns True, then I want to change the name of files within the target subfolder3 and transfer all files to another folder.
Bellow is my code. It is quite cumbersome and there is probably better ways of doing it. I tried using os.walk() and this is the closest I got to a solution but it won't move the files.
import os
import shutil
def organizer(parent_dir, target_dir, destination_dir):
for root, dirs, files in os.walk(parent_dir):
if root.endswith(target_dir):
target = root
for files in os.listdir(target):
if not files.startswith("."):
# this is to change the name of the file
fullname = files.split(".")
just_name = fullname[0]
csv_extension = fullname[1]
gz_extension = fullname[2]
subject_id = target
#make a new name
origin = subject_id + "/"+ just_name + "." + csv_extension + "." + gz_extension
#make a path based on this new name
new_name = os.path.join(destination_dir, origin)
#move file from origin folder to destination folder and rename the file
shutil.move(origin, new_name)
Any suggestions on how to make this work and / or more eficient?
simply enough, you can use the built-in os module, with os.walk(path) returns you root directories and files found
import os
for root, _, files in os.walk(path):
#your code here
for your problem, do this
import os
for root, dirs, files in os.walk(parent_directory);
for file in files:
#exctract the data from the "file"
check this for more information os.walk()
and if you want to get the name of the file, you can use os.path.basename(path)
you can even check for just the gzipped csv files you're looking for using built-in fnmatch module
import fnmathch, os
def find_csv_files(path):
result = []
for root, _, files in os.walk(path):
for name in files:
if fnmatch.fnmatch(name, "*.csv.gz"): # find csv.gz using regex paterns
result.append(os.path.join(root, name))
return list(set(results)) #to get the unique paths if for some reason duplicated
Ok, guys, I was finally able to find a solution. Here it is. Not the cleanest one, but it works in my case. Thanks for the help.
def organizer(parent_dir, target_dir, destination_dir):
for root, dirs, files in os.walk(parent_dir):
if root.endswith(target_dir):
target = root
for files in os.listdir(target):
#this one because I have several .DS store files in the folder which I don't want to extract
if not files.startswith("."):
fullname = files.split(".")
just_name = fullname[0]
csv_extension = fullname[1]
gz_extension = fullname[2]
origin = target + "/" + files
full_folder_name = origin.split("/")
#make a new name
new_name = full_folder_name[5] + "_"+ just_name + "." + csv_extension + "." + gz_extension
#make a path based on this new name
new_path = os.path.join(destination_dir, new_name)
#move file from origin folder to destination folder and rename the file
shutil.move(origin, new_path)
The guess the problem was that was passing a variable that was a renamed file (in my example, I wrongly called this variable origin) as the origin path to shutil.move(). Since this path does not exist, then the files weren't moved.
I'd like to browse through the current folder and all its subfolders and get all the files with .htm|.html extensions. I have found out that it is possible to find out whether an object is a dir or file like this:
import os
dirList = os.listdir("./") # current directory
for dir in dirList:
if os.path.isdir(dir) == True:
# I don't know how to get into this dir and do the same thing here
else:
# I got file and i can regexp if it is .htm|html
and in the end, I would like to have all the files and their paths in an array. Is something like that possible?
You can use os.walk() to recursively iterate through a directory and all its subdirectories:
for root, dirs, files in os.walk(path):
for name in files:
if name.endswith((".html", ".htm")):
# whatever
To build a list of these names, you can use a list comprehension:
htmlfiles = [os.path.join(root, name)
for root, dirs, files in os.walk(path)
for name in files
if name.endswith((".html", ".htm"))]
I had a similar thing to work on, and this is how I did it.
import os
rootdir = os.getcwd()
for subdir, dirs, files in os.walk(rootdir):
for file in files:
#print os.path.join(subdir, file)
filepath = subdir + os.sep + file
if filepath.endswith(".html"):
print (filepath)
Hope this helps.
In python 3 you can use os.scandir():
def dir_scan(path):
for i in os.scandir(path):
if i.is_file():
print('File: ' + i.path)
elif i.is_dir():
print('Folder: ' + i.path)
dir_scan(i.path)
Use newDirName = os.path.abspath(dir) to create a full directory path name for the subdirectory and then list its contents as you have done with the parent (i.e. newDirList = os.listDir(newDirName))
You can create a separate method of your code snippet and call it recursively through the subdirectory structure. The first parameter is the directory pathname. This will change for each subdirectory.
This answer is based on the 3.1.1 version documentation of the Python Library. There is a good model example of this in action on page 228 of the Python 3.1.1 Library Reference (Chapter 10 - File and Directory Access).
Good Luck!
Slightly altered version of Sven Marnach's solution..
import os
folder_location = 'C:\SomeFolderName'
file_list = create_file_list(folder_location)
def create_file_list(path):
return_list = []
for filenames in os.walk(path):
for file_list in filenames:
for file_name in file_list:
if file_name.endswith((".txt")):
return_list.append(file_name)
return return_list
There are two ways works for me.
1. Work with the `os` package and use `'__file__'` to replace the main
directory when the project locates
import os
script_dir = os.path.dirname(__file__)
path = 'subdirectory/test.txt'
file = os.path.join(script_dir, path)
fileread = open(file,'r')
2. By using '\\' to read or write the file in subfolder
fileread = open('subdirectory\\test.txt','r')
from tkinter import *
import os
root = Tk()
file = filedialog.askdirectory()
changed_dir = os.listdir(file)
print(changed_dir)
root.mainloop()
This is my current (from a Jupyter notebook) code for renaming some text files.
The issue is when I run the code, the renamed files are placed in my current working Jupyter folder. I would like the files to stay in the original folder
import glob
import os
path = 'C:\data_research\text_test\*.txt'
files = glob.glob(r'C:\data_research\text_test\*.txt')
for file in files:
os.rename(file, file[-27:])
You should only change the name and keep the path the same. Your filename will not always be longer than 27 so putting this into you code is not ideal. What you want is something that just separates the name from the path, no matter the name, no matter the path. Something like:
import os
import glob
path = 'C:\data_research\text_test\*.txt'
files = glob.glob(r'C:\data_research\text_test\*.txt')
for file in files:
old_name = os.path.basename(file) # now this is just the name of your file
# now you can do something with the name... here i'll just add new_ to it.
new_name = 'new_' + old_name # or do something else with it
new_file = os.path.join(os.path.dirname(file), new_name) # now we put the path and the name together again
os.rename(file, new_file) # and now we rename.
If you are using windows you might want to use the ntpath package instead.
file[-27:] takes the last 27 characters of the filename so unless all of your filenames are 27 characters long, it will fail. If it does succeed, you've stripped off the target directory name so the file is moved to your current directory. os.path has utilities to manage file names and you should use them:
import glob
import os
path = 'C:\data_research\text_test*.txt'
files = glob.glob(r'C:\data_research\text_test*.txt')
for file in files:
dirname, basename = os.path.split(file)
# I don't know how you want to rename so I made something up
newname = basename + '.bak'
os.rename(file, os.path.join(dirname, newname))
I'd like to browse through the current folder and all its subfolders and get all the files with .htm|.html extensions. I have found out that it is possible to find out whether an object is a dir or file like this:
import os
dirList = os.listdir("./") # current directory
for dir in dirList:
if os.path.isdir(dir) == True:
# I don't know how to get into this dir and do the same thing here
else:
# I got file and i can regexp if it is .htm|html
and in the end, I would like to have all the files and their paths in an array. Is something like that possible?
You can use os.walk() to recursively iterate through a directory and all its subdirectories:
for root, dirs, files in os.walk(path):
for name in files:
if name.endswith((".html", ".htm")):
# whatever
To build a list of these names, you can use a list comprehension:
htmlfiles = [os.path.join(root, name)
for root, dirs, files in os.walk(path)
for name in files
if name.endswith((".html", ".htm"))]
I had a similar thing to work on, and this is how I did it.
import os
rootdir = os.getcwd()
for subdir, dirs, files in os.walk(rootdir):
for file in files:
#print os.path.join(subdir, file)
filepath = subdir + os.sep + file
if filepath.endswith(".html"):
print (filepath)
Hope this helps.
In python 3 you can use os.scandir():
def dir_scan(path):
for i in os.scandir(path):
if i.is_file():
print('File: ' + i.path)
elif i.is_dir():
print('Folder: ' + i.path)
dir_scan(i.path)
Use newDirName = os.path.abspath(dir) to create a full directory path name for the subdirectory and then list its contents as you have done with the parent (i.e. newDirList = os.listDir(newDirName))
You can create a separate method of your code snippet and call it recursively through the subdirectory structure. The first parameter is the directory pathname. This will change for each subdirectory.
This answer is based on the 3.1.1 version documentation of the Python Library. There is a good model example of this in action on page 228 of the Python 3.1.1 Library Reference (Chapter 10 - File and Directory Access).
Good Luck!
Slightly altered version of Sven Marnach's solution..
import os
folder_location = 'C:\SomeFolderName'
file_list = create_file_list(folder_location)
def create_file_list(path):
return_list = []
for filenames in os.walk(path):
for file_list in filenames:
for file_name in file_list:
if file_name.endswith((".txt")):
return_list.append(file_name)
return return_list
There are two ways works for me.
1. Work with the `os` package and use `'__file__'` to replace the main
directory when the project locates
import os
script_dir = os.path.dirname(__file__)
path = 'subdirectory/test.txt'
file = os.path.join(script_dir, path)
fileread = open(file,'r')
2. By using '\\' to read or write the file in subfolder
fileread = open('subdirectory\\test.txt','r')
from tkinter import *
import os
root = Tk()
file = filedialog.askdirectory()
changed_dir = os.listdir(file)
print(changed_dir)
root.mainloop()
I have a C++/Obj-C background and I am just discovering Python (been writing it for about an hour).
I am writing a script to recursively read the contents of text files in a folder structure.
The problem I have is the code I have written will only work for one folder deep. I can see why in the code (see #hardcoded path), I just don't know how I can move forward with Python since my experience with it is only brand new.
Python Code:
import os
import sys
rootdir = sys.argv[1]
for root, subFolders, files in os.walk(rootdir):
for folder in subFolders:
outfileName = rootdir + "/" + folder + "/py-outfile.txt" # hardcoded path
folderOut = open( outfileName, 'w' )
print "outfileName is " + outfileName
for file in files:
filePath = rootdir + '/' + file
f = open( filePath, 'r' )
toWrite = f.read()
print "Writing '" + toWrite + "' to" + filePath
folderOut.write( toWrite )
f.close()
folderOut.close()
Make sure you understand the three return values of os.walk:
for root, subdirs, files in os.walk(rootdir):
has the following meaning:
root: Current path which is "walked through"
subdirs: Files in root of type directory
files: Files in root (not in subdirs) of type other than directory
And please use os.path.join instead of concatenating with a slash! Your problem is filePath = rootdir + '/' + file - you must concatenate the currently "walked" folder instead of the topmost folder. So that must be filePath = os.path.join(root, file). BTW "file" is a builtin, so you don't normally use it as variable name.
Another problem are your loops, which should be like this, for example:
import os
import sys
walk_dir = sys.argv[1]
print('walk_dir = ' + walk_dir)
# If your current working directory may change during script execution, it's recommended to
# immediately convert program arguments to an absolute path. Then the variable root below will
# be an absolute path as well. Example:
# walk_dir = os.path.abspath(walk_dir)
print('walk_dir (absolute) = ' + os.path.abspath(walk_dir))
for root, subdirs, files in os.walk(walk_dir):
print('--\nroot = ' + root)
list_file_path = os.path.join(root, 'my-directory-list.txt')
print('list_file_path = ' + list_file_path)
with open(list_file_path, 'wb') as list_file:
for subdir in subdirs:
print('\t- subdirectory ' + subdir)
for filename in files:
file_path = os.path.join(root, filename)
print('\t- file %s (full path: %s)' % (filename, file_path))
with open(file_path, 'rb') as f:
f_content = f.read()
list_file.write(('The file %s contains:\n' % filename).encode('utf-8'))
list_file.write(f_content)
list_file.write(b'\n')
If you didn't know, the with statement for files is a shorthand:
with open('filename', 'rb') as f:
dosomething()
# is effectively the same as
f = open('filename', 'rb')
try:
dosomething()
finally:
f.close()
If you are using Python 3.5 or above, you can get this done in 1 line.
import glob
# root_dir needs a trailing slash (i.e. /root/dir/)
for filename in glob.iglob(root_dir + '**/*.txt', recursive=True):
print(filename)
As mentioned in the documentation
If recursive is true, the pattern '**' will match any files and zero or more directories and subdirectories.
If you want every file, you can use
import glob
for filename in glob.iglob(root_dir + '**/**', recursive=True):
print(filename)
Agree with Dave Webb, os.walk will yield an item for each directory in the tree. Fact is, you just don't have to care about subFolders.
Code like this should work:
import os
import sys
rootdir = sys.argv[1]
for folder, subs, files in os.walk(rootdir):
with open(os.path.join(folder, 'python-outfile.txt'), 'w') as dest:
for filename in files:
with open(os.path.join(folder, filename), 'r') as src:
dest.write(src.read())
TL;DR: This is the equivalent to find -type f to go over all files in all folders below and including the current one:
for currentpath, folders, files in os.walk('.'):
for file in files:
print(os.path.join(currentpath, file))
As already mentioned in other answers, os.walk() is the answer, but it could be explained better. It's quite simple! Let's walk through this tree:
docs/
└── doc1.odt
pics/
todo.txt
With this code:
for currentpath, folders, files in os.walk('.'):
print(currentpath)
The currentpath is the current folder it is looking at. This will output:
.
./docs
./pics
So it loops three times, because there are three folders: the current one, docs, and pics. In every loop, it fills the variables folders and files with all folders and files. Let's show them:
for currentpath, folders, files in os.walk('.'):
print(currentpath, folders, files)
This shows us:
# currentpath folders files
. ['pics', 'docs'] ['todo.txt']
./pics [] []
./docs [] ['doc1.odt']
So in the first line, we see that we are in folder ., that it contains two folders namely pics and docs, and that there is one file, namely todo.txt. You don't have to do anything to recurse into those folders, because as you see, it recurses automatically and just gives you the files in any subfolders. And any subfolders of that (though we don't have those in the example).
If you just want to loop through all files, the equivalent of find -type f, you can do this:
for currentpath, folders, files in os.walk('.'):
for file in files:
print(os.path.join(currentpath, file))
This outputs:
./todo.txt
./docs/doc1.odt
The pathlib library is really great for working with files. You can do a recursive glob on a Path object like so.
from pathlib import Path
for elem in Path('/path/to/my/files').rglob('*.*'):
print(elem)
import glob
import os
root_dir = <root_dir_here>
for filename in glob.iglob(root_dir + '**/**', recursive=True):
if os.path.isfile(filename):
with open(filename,'r') as file:
print(file.read())
**/** is used to get all files recursively including directory.
if os.path.isfile(filename) is used to check if filename variable is file or directory, if it is file then we can read that file.
Here I am printing file.
If you want a flat list of all paths under a given dir (like find . in the shell):
files = [
os.path.join(parent, name)
for (parent, subdirs, files) in os.walk(YOUR_DIRECTORY)
for name in files + subdirs
]
To only include full paths to files under the base dir, leave out + subdirs.
I've found the following to be the easiest
from glob import glob
import os
files = [f for f in glob('rootdir/**', recursive=True) if os.path.isfile(f)]
Using glob('some/path/**', recursive=True) gets all files, but also includes directory names. Adding the if os.path.isfile(f) condition filters this list to existing files only
For my taste os.walk() is a little too complicated and verbose. You can do the accepted answer cleaner by:
all_files = [str(f) for f in pathlib.Path(dir_path).glob("**/*") if f.is_file()]
with open(outfile, 'wb') as fout:
for f in all_files:
with open(f, 'rb') as fin:
fout.write(fin.read())
fout.write(b'\n')
use os.path.join() to construct your paths - It's neater:
import os
import sys
rootdir = sys.argv[1]
for root, subFolders, files in os.walk(rootdir):
for folder in subFolders:
outfileName = os.path.join(root,folder,"py-outfile.txt")
folderOut = open( outfileName, 'w' )
print "outfileName is " + outfileName
for file in files:
filePath = os.path.join(root,file)
toWrite = open( filePath).read()
print "Writing '" + toWrite + "' to" + filePath
folderOut.write( toWrite )
folderOut.close()
os.walk does recursive walk by default. For each dir, starting from root it yields a 3-tuple (dirpath, dirnames, filenames)
from os import walk
from os.path import splitext, join
def select_files(root, files):
"""
simple logic here to filter out interesting files
.py files in this example
"""
selected_files = []
for file in files:
#do concatenation here to get full path
full_path = join(root, file)
ext = splitext(file)[1]
if ext == ".py":
selected_files.append(full_path)
return selected_files
def build_recursive_dir_tree(path):
"""
path - where to begin folder scan
"""
selected_files = []
for root, dirs, files in walk(path):
selected_files += select_files(root, files)
return selected_files
I think the problem is that you're not processing the output of os.walk correctly.
Firstly, change:
filePath = rootdir + '/' + file
to:
filePath = root + '/' + file
rootdir is your fixed starting directory; root is a directory returned by os.walk.
Secondly, you don't need to indent your file processing loop, as it makes no sense to run this for each subdirectory. You'll get root set to each subdirectory. You don't need to process the subdirectories by hand unless you want to do something with the directories themselves.
Try this:
import os
import sys
for root, subdirs, files in os.walk(path):
for file in os.listdir(root):
filePath = os.path.join(root, file)
if os.path.isdir(filePath):
pass
else:
f = open (filePath, 'r')
# Do Stuff
If you prefer an (almost) Oneliner:
from pathlib import Path
lookuppath = '.' #use your path
filelist = [str(item) for item in Path(lookuppath).glob("**/*") if Path(item).is_file()]
In this case you will get a list with just the paths of all files located recursively under lookuppath.
Without str() you will get PosixPath() added to each path.
This worked for me:
import glob
root_dir = "C:\\Users\\Scott\\" # Don't forget trailing (last) slashes
for filename in glob.iglob(root_dir + '**/*.jpg', recursive=True):
print(filename)
# do stuff
If just the file names are not enough, it's easy to implement a Depth-first search on top of os.scandir():
stack = ['.']
files = []
total_size = 0
while stack:
dirname = stack.pop()
with os.scandir(dirname) as it:
for e in it:
if e.is_dir():
stack.append(e.path)
else:
size = e.stat().st_size
files.append((e.path, size))
total_size += size
The docs have this to say:
The scandir() function returns directory entries along with file attribute information, giving better performance for many common use cases.