I have a Python script that reads through a text csv file and creates a playlist file. However I can only do one at a time, like:
python playlist.py foo.csv foolist.txt
However, I have a directory of files that need to be made into a playlist, with different names, and sometimes a different number of files.
So far I have looked at creating a txt file with a list of all the names of the file in the directory, then loop through each line of that, however I know there must be an easier way to do it.
for f in *.csv; do
python playlist.py "$f" "${f%.csv}list.txt"
done
Will that do the trick? This will put foo.csv in foolist.txt and abc.csv in abclist.txt.
Or do you want them all in the same file?
Just use a for loop with the asterisk glob, making sure you quote things appropriately for spaces in filenames
for file in *.csv; do
python playlist.py "$file" >> outputfile.txt;
done
Is it a single directory, or nested?
Ex.
topfile.csv
topdir
--dir1
--file1.csv
--file2.txt
--dir2
--file3.csv
--file4.csv
For nested, you can use os.walk(topdir) to get all the files and dirs recursively within a directory.
You could set up your script to accept dirs or files:
python playlist.py topfile.csv topdir
import sys
import os
def main():
files_toprocess = set()
paths = sys.argv[1:]
for p in paths:
if os.path.isfile(p) and p.endswith('.csv'):
files_toprocess.add(p)
elif os.path.isdir(p):
for root, dirs, files in os.walk(p):
files_toprocess.update([os.path.join(root, f)
for f in files if f.endswith('.csv')])
if you have directory name you can use os.listdir
os.listdir(dirname)
if you want to select only a certain type of file, e.g., only csv file you could use glob module.
Related
I've got 2 folders, each with a different CSV file inside (both have the same format):
I've written some python code to search within the "C:/Users/Documents" directory for CSV files which begin with the word "File"
import glob, os
inputfile = []
for root, dirs, files in os.walk("C:/Users/Documents/"):
for datafile in files:
if datafile.startswith("File") and datafile.endswith(".csv"):
inputfile.append([os.path.join(root, datafile)])
print(inputfile)
That almost worked as it returns:
[['C:/Users/Documents/Test A\\File 1.csv'], ['C:/Users/Documents/Test B\\File 2.csv']]
Is there any way I can get it to return this instead (no sub list and shows / instead of \):
['C:/Users/Documents/Test A/File 1.csv', 'C:/Users/Documents/Test B/File 2.csv']
The idea is so I can then read both CSV files at once later, but I believe I need to get the list in the format above first.
okay, I will paste an option here.
I made use of os.path.abspath to get the the path before join.
Have a look and see if it works.
import os
filelist = []
for folder, subfolders, files in os.walk("C:/Users/Documents/"):
for datafile in files:
if datafile.startswith("File") and datafile.endswith(".csv"):
filePath = os.path.abspath(os.path.join(folder, datafile))
filelist.append(filePath)
filelist
Result:
['C:/Users/Documents/Test A/File 1.csv','C:/Users/Documents/Test B/File 2.csv']
I am combining two questions here because they are related to each other.
Question 1: I am trying to use glob to open all the files in a folder but it is giving me "Syntax Error". I am using Python 3.xx. Has the syntax changed for Python 3.xx?
Error Message:
File "multiple_files.py", line 29
files = glob.glob(/src/xyz/rte/folder/)
SyntaxError: invalid syntax
Code:
import csv
import os
import glob
from pandas import DataFrame, read_csv
#extracting
files = glob.glob(/src/xyz/rte/folder/)
for fle in files:
with open (fle) as f:
print("output" + fle)
f_read.close()
Question 2: I want to read input files, append "output" to the names and print out the names of the files. How can I do that?
Example: Input file name would be - xyz.csv and the code should print output_xyz.csv .
Your help is appreciated.
Your first problem is that strings, including pathnames, need to be in quotes. This:
files = glob.glob(/src/xyz/rte/folder/)
… is trying to divide a bunch of variables together, but the leftmost and rightmost divisions are missing operands, so you've confused the parser. What you want is this:
files = glob.glob('/src/xyz/rte/folder/')
Your next problem is that this glob pattern doesn't have any globs in it, so the only thing it's going to match is the directory itself.
That's perfectly legal, but kind of useless.
And then you try to open each match as a text file. Which you can't do with a directory, hence the IsADirectoryError.
The answer here is less obvious, because it's not clear what you want.
Maybe you just wanted all of the files in that directory? In that case, you don't want glob.glob, you want listdir (or maybe scandir): os.listdir('/src/xyz/rte/folder/').
Maybe you wanted all of the files in that directory or any of its subdirectories? In that case, you could do it with rglob, but os.walk is probably clearer.
Maybe you did want all the files in that directory that match some pattern, so glob.glob is right—but in that case, you need to specify what that pattern is. For example, if you wanted all .csv files, that would be glob.glob('/src/xyz/rte/folder/*.csv').
Finally, you say "I want to read input files, append "output" to the names and print out the names of the files". Why do you want to read the files if you're not doing anything with the contents? You can do that, of course, but it seems pretty wasteful. If you just want to print out the filenames with output appended, that's easy:
for filename in os.listdir('/src/xyz/rte/folder/'):
print('output'+filename)
This works in http://pyfiddle.io:
Doku: https://docs.python.org/3/library/glob.html
import csv
import os
import glob
# create some files
for n in ["a","b","c","d"]:
with open('{}.txt'.format(n),"w") as f:
f.write(n)
print("\nFiles before")
# get all files
files = glob.glob("./*.*")
for fle in files:
print(fle) # print file
path,fileName = os.path.split(fle) # split name from path
# open file for read and second one for write with modified name
with open (fle) as f,open('{}{}output_{}'.format(path,os.sep, fileName),"w") as w:
content = f.read() # read all
w.write(content.upper()) # write all modified
# check files afterwards
print("\nFiles after")
files = glob.glob("./*.*") # pattern for all files
for fle in files:
print(fle)
Output:
Files before
./d.txt
./main.py
./c.txt
./b.txt
./a.txt
Files after
./d.txt
./output_c.txt
./output_d.txt
./main.py
./output_main.py
./c.txt
./b.txt
./output_b.txt
./a.txt
./output_a.txt
I am on windows and would use os.walk (Doku) instead.
for d,subdirs,files in os.walk("./"): # deconstruct returned aktDir, all subdirs, files
print("AktDir:", d)
print("Subdirs:", subdirs)
print("Files:", files)
Output:
AktDir: ./
Subdirs: []
Files: ['d.txt', 'output_c.txt', 'output_d.txt', 'main.py', 'output_main.py',
'c.txt', 'b.txt', 'output_b.txt', 'a.txt', 'output_a.txt']
It also recurses into subdirs.
I am new to python. I have successful written a script to search for something within a file using :
open(r"C:\file.txt) and re.search function and all works fine.
Is there a way to do the search function with all files within a folder? Because currently, I have to manually change the file name of my script by open(r"C:\file.txt),open(r"C:\file1.txt),open(r"C:\file2.txt)`, etc.
Thanks.
You can use os.walk to check all the files, as the following:
import os
for root, _, files in os.walk(path):
for filename in files:
with open(os.path.join(root, filename), 'r') as f:
#your code goes here
Explanation:
os.walk returns tuple of (root path, dir names, file names) in the folder, so you can iterate through filenames and open each file by using os.path.join(root, filename) which basically joins the root path with the file name so you can open the file.
Since you're a beginner, I'll give you a simple solution and walk through it.
Import the os module, and use the os.listdir function to create a list of everything in the directory. Then, iterate through the files using a for loop.
Example:
# Importing the os module
import os
# Give the directory you wish to iterate through
my_dir = <your directory - i.e. "C:\Users\bleh\Desktop\files">
# Using os.listdir to create a list of all of the files in dir
dir_list = os.listdir(my_dir)
# Use the for loop to iterate through the list you just created, and open the files
for f in dir_list:
# Whatever you want to do to all of the files
If you need help on the concepts, refer to the following:
for looops in p3: http://www.python-course.eu/python3_for_loop.php
os function Library (this has some cool stuff in it): https://docs.python.org/2/library/os.html
Good luck!
You can use the os.listdir(path) function:
import os
path = '/Users/ricardomartinez/repos/Salary-API'
# List for all files in a given PATH
file_list = os.listdir(path)
# If you want to filter by file type
file_list = [file for file in os.listdir(path) if os.path.splitext(file)[1] == '.py']
# Both cases yo can iterate over the list and apply the operations
# that you have
for file in file_list:
print(file)
#Operations that you want to do over files
I have a large numbers of fasta files (these are just text files) in different subfolders. What I need is a way to search through the directories for files that have the same name and concatenate these into a file with the name of the input files. I can't do this manually as I have 10000+ genes that I need to do this for.
So far I have the following Python code that looks through one of the directories and then uses those file names to search through the other directories. This returns a list that has the full path for each file.
import os
from os.path import join, abspath
path = '/directoryforfilelist/' #Directory for source list
listing = os.listdir(path)
for x in listing:
for root, dirs, files in os.walk('/rootdirectorytosearch/'):
if x in files:
pathlist = abspath(join(root,x))
Where I am stuck is how to concatenate the files it returns that have the same name. The results from this script look like this.
/directory1/file1.fasta
/directory2/file1.fasta
/directory3/file1.fasta
/directory1/file2.fasta
/directory2/file2.fasta
/directory3/file2.fasta
In this case I would need the end result to be two files named file1.fasta and file2.fasta that contain the text from each of the same named files.
Any leads on where to go from here would be appreciated. While I did this part in Python anyway that gets the job done is fine with me. This is being run on a Mac if that matters.
Not tested, but here's roughly what I'd do:
from itertools import groupby
import os
def conc_by_name(names):
for tail, group in groupby(names, key=os.path.split):
with open(tail, 'w') as out:
for name in group:
with open(name) as f:
out.writelines(f)
This will create the files (file1.fasta and file2.fasta in your example) in the current folder.
For each file of your list, allocate the target file in append mode, read each line of your source file and write it to the target file.
Assuming that the target folder is empty to start with, and is not in /rootdirectorytosearch.
I want to implement a file reader (folders and subfolders) script which detects some tags and delete those tags from the files.
The files are .cpp, .h .txt and .xml And they are hundreds of files under same folder.
I have no idea about python, but people told me that I can do it easily.
EXAMPLE:
My main folder is A: C:\A
Inside A, I have folders (B,C,D) and some files A.cpp A.h A.txt and A.xml. In B i have folders B1, B2,B3 and some of them have more subfolders, and files .cpp, .xml and .h....
xml files, contains some tags like <!-- $Mytag: some text$ -->
.h and .cpp files contains another kind of tags like //$TAG some text$
.txt has different format tags: #$This is my tag$
It always starts and ends with $ symbol but it always have a comment character (//,
The idea is to run one script and delete all tags from all files so the script must:
Read folders and subfolders
Open files and find tags
If they are there, delete and save files with changes
WHAT I HAVE:
import os
for root, dirs, files in os.walk(os.curdir):
if files.endswith('.cpp'):
%Find //$ and delete until next $
if files.endswith('.h'):
%Find //$ and delete until next $
if files.endswith('.txt'):
%Find #$ and delete until next $
if files.endswith('.xml'):
%Find <!-- $ and delete until next $ and -->
The general solution would be to:
use the os.walk() function to traverse the directory tree.
Iterate over the filenames and use fn_name.endswith('.cpp') with if/elseif to determine which file you're working with
Use the re module to create a regular expression you can use to determine if a line contains your tag
Open the target file and a temporary file (use the tempfile module). Iterate over the source file line by line and output the filtered lines to your tempfile.
If any lines were replaced, use os.unlink() plus os.rename() to replace your original file
It's a trivial excercise for a Python adept but for someone new to the language, it'll probably take a few hours to get working. You probably couldn't ask for a better task to get introduced to the language though. Good Luck!
----- Update -----
The files attribute returned by os.walk is a list so you'll need to iterate over it as well. Also, the files attribute will only contain the base name of the file. You'll need to use the root value in conjunction with os.path.join() to convert this to a full path name. Try doing just this:
for root, d, files in os.walk('.'):
for base_filename in files:
full_name = os.path.join(root, base_filename)
if full_name.endswith('.h'):
print full_name, 'is a header!'
elif full_name.endswith('.cpp'):
print full_name, 'is a C++ source file!'
If you're using Python 3, the print statements will need to be function calls but the general idea remains the same.
Try something like this:
import os
import re
CPP_TAG_RE = re.compile(r'(?<=// *)\$[^$]+\$')
tag_REs = {
'.h': CPP_TAG_RE,
'.cpp': CPP_TAG_RE,
'.xml': re.compile(r'(?<=<!-- *)\$[^$]+\$(?= *-->)'),
'.txt': re.compile(r'(?<=# *)\$[^$]+\$'),
}
def process_file(filename, regex):
# Set up.
tempfilename = filename + '.tmp'
infile = open(filename, 'r')
outfile = open(tempfilename, 'w')
# Filter the file.
for line in infile:
outfile.write(regex.sub("", line))
# Clean up.
infile.close()
outfile.close()
# Enable only one of the two following lines.
os.rename(filename, filename + '.orig')
#os.remove(filename)
os.rename(tempfilename, filename)
def process_tree(starting_point=os.curdir):
for root, d, files in os.walk(starting_point):
for filename in files:
# Get rid of `.lower()` in the following if case matters.
ext = os.path.splitext(filename)[1].lower()
if ext in tag_REs:
process_file(os.path.join(root, base_filename), tag_REs[ext])
Nice thing about os.splitext is that it does the right thing for filenames that start with a ..