How to Capture STDERR Output from a Subprocess in Python

Learn how to properly capture the STDERR output generated by subprocesses in Python, instead of the STDOUT, which may not provide the desired information.
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How to Capture STDERR Output from a Subprocess in Python

When running external commands in Python using subprocesses, you may sometimes find that the output displayed in the terminal isn't what you're looking for. Instead of capturing useful information from stdout, you may need to capture that from stderr. This article will explain how you can capture contents generated during a process run by the subprocess module.

The Problem

You might have encountered a situation where your code looks like this:

[[See Video to Reveal this Text or Code Snippet]]

When you run this code, you see output in the terminal that contains important information, such as:

[[See Video to Reveal this Text or Code Snippet]]

However, this information is not being captured in your output collection when you use stdout.

Understanding the Solution

Switch from stdout to stderr

The first thing you’ll need to do is change the way you're capturing output. Instead of stdout, you should focus on the stderr stream. Here's how you can modify your original code:

[[See Video to Reveal this Text or Code Snippet]]

Explanation of the Code

from subprocess import run, PIPE: This line imports the necessary functions from the subprocess module.

run() function: This is used to run a command. Unlike Popen, it’s simpler and is suitable for most use cases.

stderr=PIPE: This captures the error output generated by the command.

text=True: This parameter ensures that the output is captured as a string instead of bytes.

Handling Raw Bytes

If you want the output in its raw byte format instead of a string, simply remove the text=True flag:

[[See Video to Reveal this Text or Code Snippet]]

Writing the Output to a File

If you want to direct the error output to a file instead of printing it, you can easily do that:

[[See Video to Reveal this Text or Code Snippet]]

Conclusion

Capturing contents generated by a subprocess can be tricky, especially when the output you need is not in stdout. By switching your focus to stderr, you can successfully capture and process the information you require. Whether it’s printing to the console, processing as bytes, or saving to a file, Python’s subprocess capabilities can help you achieve your goals efficiently and effectively.

Now you can take full advantage of the subprocess module in Python for your bioinformatics tasks or any other command-line process you wish to automate. Happy coding!