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open a folder to then use the files in python correctly

Usually I navigate to the folder I am extracting data from and copy the file name directly:
df2=pd.read_csv('10_90_bnOH-MEA.csv',usecols=[1])
If I have multiple files and want to do the same for all the files, how do I specify the folder to open and get all the files inside?
I want to run the above code without specifying the file's full path
(C:\Users\X\Desktop\Y\Z\10_90_bnOH-MEA.csv)

You want listdir from the os module.
import os
path = "C:\\Users\\X\\Desktop\\Y\\Z\\"
files = os.listdir(path)
print(files)
dataframe_list = []
for filename in files:
dataframe_list.append(pd.read_csv(os.path.join(path,filename)))

You should open the desired directory and loop through all the files then do something to them.
# import required module
import os
# assign directory
directory = 'files'
# iterate over files in
def goThroughDirectory(directory):
for filename in os.listdir(directory):
f = os.path.join(directory, filename)
# checking if it is a file
if os.path.isfile(f):
# do something
If you also want to loop through all the files in a directory you should add a check for if os.path.isdir(f) like this
...
def goThroughDirectory(directory):
for filename in os.listdir(directory):
f = os.path.join(directory, filename)
# checking if it is a file
if os.path.isfile(f):
# do something
elif os.path.isdir(f):
# its not a file but a directory then loop through that directory aswell
goThroughDirectory(directory + "\" + f)
for more information you should check geeksforgeeks

Find directories missing .csv file in Python

I have ~1000 directories, containing various .csv files within them. I am trying to check if a specific type of csv file, containing a filename that begins with PTSD_OCOTBER, exists in each directory.
If this file does not exist in the directory, I want to print out that directory into a .txt file.
Here is what I have so far.
import os,sys,time,shutil
import subprocess
#determine filetype to look for.
file_type = ".csv"
print("Running file counter for" + repr(file_type))
#for each folder in the root directory
for subdir, dirs, files in os.walk(rootdir):
if("GeneSet" in subdir):
folder_name = subdir.rsplit('/', 1)[-1] #get the folder name.
for f in files:
#unclear how to write this part.
#how to tell if no files exist in directory?
This successfully finds the .csv files of interest, but how do achieve the above?

So files is the list of files in that directory that you are currently walking. You want to know if there are no files that start with PTSD_OCOTBER (PTSD_OCTOBER ?):
for subdir, dirs, files in os.walk(rootdir):
if("GeneSet" in subdir):
folder_name = subdir.rsplit('/', 1)[-1] #get the folder name.
dir_of_interest = not any(f.startswith('PTSD_OCOTBER') for f in files)
if dir_of_interest:
# do stuff with folder_name
Now you want to save the results into a text file? If you have a Unix-style computer, then you can use output redirection on your terminal, such as
python3 fileanalysis.py > result.txt
after writing print(folder_name) instead of # do stuff with folder_name.
Or you can use Python itself to write the file, such as:
found_dirs = []
for subdir, dirs, files in os.walk(rootdir):
...
if dir_of_interest:
found_dirs.append(folder_name)
with open('result.txt', 'w') as f:
f.write('\n'.join(found_dirs))

Copying files in python using shutil

I have the following directory structure:
-mailDir
-folderA
-sub1
-sub2
-inbox
-1.txt
-2.txt
-89.txt
-subInbox
-subInbox2
-folderB
-sub1
-sub2
-inbox
-1.txt
-2.txt
-200.txt
-577.txt
The aim is to copy all the txt files under inbox folder into another folder.
For this I tried the below code
import os
from os import path
import shutil
rootDir = "mailDir"
destDir = "destFolder"
eachInboxFolderPath = []
for root, dirs, files in os.walk(rootDir):
for dirName in dirs:
if(dirName=="inbox"):
eachInboxFolderPath.append(root+"\\"+dirName)
for ii in eachInboxFolderPath:
for i in os.listdir(ii):
shutil.copy(path.join(ii,i),destDir)
If the inbox directory only has .txt files then the above code works fine. Since the inbox folder under folderA directory has other sub directory along with .txt files, the code returns permission denied error. What I understood is shutil.copy won't allow to copy the folders.
The aim is to copy only the txt files in every inbox folder to some other location. If the file names are same in different inbox folder I have to keep both file names. How we can improve the code in this case ? Please note other than .txt all others are folders only.

One simple solution is to filter for any i that does not have the .txt extension by using the string endswith() method.
import os
from os import path
import shutil
rootDir = "mailDir"
destDir = "destFolder"
eachInboxFolderPath = []
for root, dirs, files in os.walk(rootDir):
for dirName in dirs:
if(dirName=="inbox"):
eachInboxFolderPath.append(root+"\\"+dirName)
for ii in eachInboxFolderPath:
for i in os.listdir(ii):
if i.endswith('.txt'):
shutil.copy(path.join(ii,i),destDir)
This should ignore any folders and non-txt files that are found with os.listdir(ii). I believe that is what you are looking for.

Just remembered that I once wrote several files to solve this exact problem before. You can find the source code here on my Github.
In short, there are two functions of interest here:
list_files(loc, return_dirs=False, return_files=True, recursive=False, valid_exts=None)
copy_files(loc, dest, rename=False)
For your case, you could copy and paste these functions into your project and modify copy_files like this:
def copy_files(loc, dest, rename=False):
# get files with full path
files = list_files(loc, return_dirs=False, return_files=True, recursive=True, valid_exts=('.txt',))
# copy files in list to dest
for i, this_file in enumerate(files):
# change name if renaming
if rename:
# replace slashes with hyphens to preserve unique name
out_file = sub(r'^./', '', this_file)
out_file = sub(r'\\|/', '-', out_file)
out_file = join(dest, out_file)
copy(this_file, out_file)
files[i] = out_file
else:
copy(this_file, dest)
return files
Then just call it like so:
copy_files('mailDir', 'destFolder', rename=True)
The renaming scheme might not be exactly what you want, but it will at least not override your files. I believe this should solve all your problems.

Here you go:
import os
from os import path
import shutil
destDir = '<absolute-path>'
for root, dirs, files in os.walk(os.getcwd()):
# Filter out only '.txt' files.
files = [f for f in files if f.endswith('.txt')]
# Filter out only 'inbox' directory.
dirs[:] = [d for d in dirs if d == 'inbox']
for f in files:
p = path.join(root, f)
# print p
shutil.copy(p, destDir)
Quick and simple.
sorry, I forgot the part where, you also need unique file names as well. The above solution only works for distinct file names in a single inbox folder.
For copying files from multiple inboxes and having a unique name in the destination folder, you can try this:
import os
from os import path
import shutil
sourceDir = os.getcwd()
fixedLength = len(sourceDir)
destDir = '<absolute-path>'
filteredFiles = []
for root, dirs, files in os.walk(sourceDir):
# Filter out only '.txt' files in all the inbox directories.
if root.endswith('inbox'):
# here I am joining the file name to the full path while filtering txt files
files = [path.join(root, f) for f in files if f.endswith('.txt')]
# add the filtered files to the main list
filteredFiles.extend(files)
# making a tuple of file path and file name
filteredFiles = [(f, f[fixedLength+1:].replace('/', '-')) for f in filteredFiles]
for (f, n) in filteredFiles:
print 'copying file...', f
# copying from the path to the dest directory with specific name
shutil.copy(f, path.join(destDir, n))
print 'copied', str(len(filteredFiles)), 'files to', destDir
If you need to copy all files instead of just txt files, then just change the condition f.endswith('.txt') to os.path.isfile(f) while filtering out the files.

Moving files and creating directories if certain file type in python

This is probably a simple question, but I'm brand new to python and programming in general.
I'm working on a simple program to copy/move .mp3 files from on location to another while mirroring the directory structure of the source location. What I have so far works, however it also creates new folders in the destination location even if the source folder contained no mp3 files. I only want to create the new directories if the source contains .mp3s, otherwise it could lead to a bunch of empty folders in the destination.
Here is what I have so far:
import os
import shutil #Used for copying files
##CONFIG
source_dir = "C:\Users\username\Desktop\iTunes\\" #set the root folder that you want to scan and move files from. This script will scan recursively.
destPath = "C:\Users\username\Desktop\converted From iTunes" #set the destination root that you want to move files to. Any non-existing sub directories will be created.
ext = ".mp3" #set the type of file you want to search for.
count = 0 #initialize counter variable to count number of files moved
##
##FIND FILES
for dirName, subdirList, fileList in os.walk(source_dir):
#set the path for the destination folder(s)
dest = destPath + dirName.replace(source_dir, '\\')
#if the source directory doesn't exist in the destination folder
#then create a new folder
if not os.path.isdir(dest):
os.mkdir(dest)
print('Directory created at: ' + dest)
for fname in fileList:
if fname.endswith(ext) :
#determine source & new file locations
oldLoc = dirName + '\\' + fname
newLoc = dest + '\\' + fname
if os.path.isfile(newLoc): # check to see if the file already exists. If it does print out a message saying so.
print ('file "' + newLoc + fname + '" already exists')
if not os.path.isfile(newLoc): #if the file doesnt exist then copy it and print out confirmation that is was copied/moved
try:
shutil.move(oldLoc, newLoc)
print('File ' + fname + ' copied.')
count = count + 1
except IOError:
print('There was an error copying the file: "' + fname + '"')
print 'error'
print "\n"
print str(count) + " files were moved."
print "\n"
so if the folder structure is something like:
root->
band 1->
album name->
song.m4a,
song2.m4a
right now it will create all those folders in the destination driectory, even though there are no .mp3s to copy.....
Any help is appreciated!

I think I would create my own wrapper around copy for this sort of thing:
def fcopy(src,dest):
"""
Copy file from source to dest. dest can include an absolute or relative path
If the path doesn't exist, it gets created
"""
dest_dir = os.path.dirname(dest)
try:
os.makedirs(dest_dir)
except os.error as e:
pass #Assume it exists. This could fail if you don't have permissions, etc...
shutil.copy(src,dest)
Now you can just walk the tree calling this function on any .mp3 file.

The simplest thing to do I can think of for your existing code would be to just make it skip over any folders that don't have any .mp3 files in them. This can easily be done by adding the following items and if statement to the top of your loop. The itertools.ifilter() and fnmatch.fnmatch() functions can be used together to simplify checking for files with the proper extension.
from itertools import ifilter
from fnmatch import fnmatch
ext = '.mp3'
fnPattern = '*'+ext
for dirName, subdirList, fileList in os.walk(source_dir):
if not any(ifilter(lambda fname: fnmatch(fname, fnPattern), fileList)):
print ' skipping "{}"'.format(dirName)
continue
...
You will also have to change the os.mkdir(dest) to os.makedirs(dest) in the code further down to ensure that any subdirectories skipped by earlier iterations get created when there's a need to copy files to a corresponding subbranch of the destination directory.
You could optimize things a bit by creating and saving a possibly empty iterator of matching files that have the extension, and then use it again later to to determine what files to copy:
from itertools import ifilter
from fnmatch import fnmatch
ext = '.mp3'
fnPattern = '*'+ext
for dirName, subdirList, fileList in os.walk(source_dir):
# generate list of files in directory with desired extension
matches = ifilter(lambda fname: fnmatch(fname, fnPattern), fileList)
# skip subdirectory if it does not contain any files of interest
if not matches:
continue
...
... create destination directory with os.makedirs()
...
# copy each file to destination directory
for fname in matches:
... copy file

Would shutils.copytree not do what you want in fewer lines?

Traversing File Directory

this is the first question I am posting on stackoverflow so excuse me if I did something out of the norm.
I am trying to create a python program which traverses a user selected directory to display all file contents of the folders selected. For example: Documents folders has several folders with files inside of them, I am trying to save all files in the Documents folder to an array.
The method below is what I am using to traverse a directory (hoping it is a simple problem)
def saveFilesToArray(dir):
allFiles = []
os.chdir(dir)
for file in glob.glob("*"):
print(file)
if (os.path.isfile(file)):
allFiles.append(file)
elif(os.path.isdir(file)):
print(dir + "/" + file + " is a directory")
allFiles.append(saveFilesToArray(dir + "/" + file))
return allFiles

This will give you just the files:
import os
def list_files(root):
all_files = []
for root, dirs, files in os.walk(root, followlinks=True):
for file in files:
full_path = os.path.join(root, file)
all_files.append(full_path)
return all_files

I hope this is helpful:
import os
def saveFilesToList(theDir):
allFiles = []
for root, dirs, files in os.walk(theDir):
for name in files:
npath = os.path.join(root,name)
if os.path.isfile(npath):
allFiles.append(npath)
return allFiles
Traverses all directories and stores the path to files (that are not directories) in the list. It seems much easier to use this than glob.