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Скачать или смотреть How to Get File Names Using the glob Function in Python

  • vlogize
  • 2025-04-13
  • 4
How to Get File Names Using the glob Function in Python
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Описание к видео How to Get File Names Using the glob Function in Python

Learn how to efficiently retrieve file names from directories using the `glob` function in Python, and the alternative `pathlib`, ensuring seamless integration with workflows like Snakemake.
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This video is based on the question https://stackoverflow.com/q/69298491/ asked by the user 'Arun Alexander' ( https://stackoverflow.com/u/16677894/ ) and on the answer https://stackoverflow.com/a/69298898/ provided by the user 'Szabolcs' ( https://stackoverflow.com/u/6337523/ ) at 'Stack Overflow' website. Thanks to these great users and Stackexchange community for their contributions.

Visit these links for original content and any more details, such as alternate solutions, latest updates/developments on topic, comments, revision history etc. For example, the original title of the Question was: How to get the names of the files using glob function in python?

Also, Content (except music) licensed under CC BY-SA https://meta.stackexchange.com/help/l...
The original Question post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/... ) license, and the original Answer post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/... ) license.

If anything seems off to you, please feel free to write me at vlogize [AT] gmail [DOT] com.
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How to Get File Names Using the glob Function in Python

When working with files in a directory, especially in data analysis tasks like the ones performed in Snakemake workflows, retrieving file names can be essential. In this guide, we’ll explore how to effectively get file names using the glob function in Python, along with an alternative that may simplify your tasks.

The Problem at Hand

Imagine you have a directory containing several FASTQ files used in bioinformatics, structured like this:

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

In your analysis, you need to extract specific parts of these file names. In this particular case, you would like to isolate the sample id (e.g., SRR01231) and the integer suffix (e.g., 1 or 2) associated with it.

You attempted to do this with the glob function, but it didn't yield the expected results:

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

A Better Solution

The good news is that there's a more efficient way to achieve your goal using the pathlib module, which streamlines filesystem paths and offers an easy way to manipulate file names. Let's dive into the solution.

Using pathlib for File Extraction

Step-by-Step Breakdown

Import the pathlib Module: This built-in module makes it easier to work with files and directories.

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

Define the Path: Specify the directory that contains your FASTQ files. Replace "/path/to/your/fastq-files" with your actual directory path.

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

Iterate Through the Files: Use a loop to go through each file path object returned by the glob method.

Extract the Required Information: Split the file name to separate the sample id from the integer.

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

Full Example Code

Bringing it all together, your complete code would look like this:

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

Benefits of Using pathlib

Readability: The code is clearer and easier to understand compared to traditional string manipulation methods.

Compatibility: It works seamlessly across different operating systems.

Conclusion

In this post, we tackled how to effectively gather file names from a directory using Python's glob function. With a detailed explanation and a practical code example utilizing pathlib, you are now equipped to easily extract sample IDs and integers from your FASTQ files.

Feeling stuck with your data workflow? Give this method a try, and don't hesitate to explore other Python capabilities to simplify your tasks!

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