How to redirect 'print' output to a file?

Question

The most obvious way to do this would be to print to a file object:

with open('out.txt', 'w') as f:
    print('Filename:', filename, file=f)  # Python 3.x
    print >> f, 'Filename:', filename     # Python 2.x

However, redirecting stdout also works for me. It is probably fine for a one-off script such as this:

import sys

orig_stdout = sys.stdout
f = open('out.txt', 'w')
sys.stdout = f

for i in range(2):
    print('i = ', i)

sys.stdout = orig_stdout
f.close()

Since Python 3.4 there's a simple context manager available to do this in the standard library:

from contextlib import redirect_stdout

with open('out.txt', 'w') as f:
    with redirect_stdout(f):
        print('data')

Redirecting externally from the shell itself is another option, and often preferable:

./script.py > out.txt

Other questions:

What is the first filename in your script? I don't see it initialized.

My first guess is that glob doesn't find any bamfiles, and therefore the for loop doesn't run. Check that the folder exists, and print out bamfiles in your script.

Also, use os.path.join and os.path.basename to manipulate paths and filenames.

You can redirect print with the file argument (in Python 2 there was the >> operator instead).

f = open(filename,'w')
print('whatever', file=f) # Python 3.x
print >>f, 'whatever'     # Python 2.x

In most cases, you're better off just writing to the file normally.

f.write('whatever')

or, if you have several items you want to write with spaces between, like print:

f.write(' '.join(('whatever', str(var2), 'etc')))

Python 2 or Python 3 API reference:

print(*objects, sep=' ', end='\n', file=sys.stdout, flush=False)

The file argument must be an object with a write(string) method; if it is not present or None, sys.stdout will be used. Since printed arguments are converted to text strings, print() cannot be used with binary mode file objects. For these, use file.write(...) instead.

Since file object normally contains write() method, all you need to do is to pass a file object into its argument.

Write/Overwrite to File

with open('file.txt', 'w') as f:
    print('hello world', file=f)

Write/Append to File

with open('file.txt', 'a') as f:
    print('hello world', file=f)

This works perfectly:

import sys
sys.stdout=open("test.txt","w")
print ("hello")
sys.stdout.close()

Now the hello will be written to the test.txt file. Make sure to close the stdout with a close, without it the content will not be save in the file

Don't use print, use logging

You can change sys.stdout to point to a file, but this is a pretty clunky and inflexible way to handle this problem. Instead of using print, use the logging module.

With logging, you can print just like you would to stdout, or you can also write the output to a file. You can even use the different message levels (critical, error, warning, info, debug) to, for example, only print major issues to the console, but still log minor code actions to a file.

A simple example

Import logging, get the logger, and set the processing level:

import logging
logger = logging.getLogger()
logger.setLevel(logging.DEBUG) # process everything, even if everything isn't printed

If you want to print to stdout:

ch = logging.StreamHandler()
ch.setLevel(logging.INFO) # or any other level
logger.addHandler(ch)

If you want to also write to a file (if you only want to write to a file skip the last section):

fh = logging.FileHandler('myLog.log')
fh.setLevel(logging.DEBUG) # or any level you want
logger.addHandler(fh)

Then, wherever you would use print use one of the logger methods:

# print(foo)
logger.debug(foo)

# print('finishing processing')
logger.info('finishing processing')

# print('Something may be wrong')
logger.warning('Something may be wrong')

# print('Something is going really bad')
logger.error('Something is going really bad')

To learn more about using more advanced logging features, read the excellent logging tutorial in the Python docs.

The easiest solution isn't through python; its through the shell. From the first line of your file (#!/usr/bin/python) I'm guessing you're on a UNIX system. Just use print statements like you normally would, and don't open the file at all in your script. When you go to run the file, instead of

./script.py

to run the file, use

./script.py > <filename>

where you replace <filename> with the name of the file you want the output to go in to. The > token tells (most) shells to set stdout to the file described by the following token.

One important thing that needs to be mentioned here is that "script.py" needs to be made executable for ./script.py to run.

So before running ./script.py,execute this command

chmod a+x script.py (make the script executable for all users)