How to redirect 'print' output to a file using python?

Question

I want to redirect the print to a .txt file using python. I have a \'for\' loop, which will \'print\' the output for each of my .bam file while I want to redirect ALL these

Answer 1

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.