How Can I Redirect Console Output to a File in Python?

Redirect Console Output to a File

In Python, redirecting the stdout stream to a file allows developers to capture and save printed output. To achieve this, the sys.stdout attribute can be manipulated. However, a recent issue has been reported where the approach outlined in the original question doesn't generate the desired output.

Problem Resolution

The problem lies in the incorrect usage of the file= parameter when printing. In Python versions 3.x and above, the correct syntax is print('Filename:', filename, file=f). For Python 2.x, use print >> f, 'Filename:', filename.

Alternatively, the with statement can be used to redirect stdout more concisely:

with open('output.txt', 'w') as f:
    with redirect_stdout(f):
        print('Filename:', filename)

Additional Methods

Besides using sys.stdout, there are other methods to redirect output:

• Using a File Object: Write directly to a file object, as shown below:

  with open('out.txt', 'w') as f:
    print('Filename:', filename, file=f)

• External Shell Redirection: Use the > operator in the shell to redirect output:

  ./script.py > out.txt

Troubleshooting

In the provided script, make sure:

• The specified path (/home/xxx/nearline/bamfiles) contains valid .bam files
• The glob.glob function correctly identifies those files
• The full path to the samtools executable is correct (/share/bin/samtools/samtools)

Improved Result

Using the corrected syntax and a file object, the expected output would be:

Filename: ERR001268.bam
Readlines finished!
Mean: 233
SD: 10
Interval is: (213, 252)

This updated version of the script captures the output and redirects it to the output.txt file.

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