Concatenating Text Files in Nested Directories with Bash
Discover how to concatenate multiple text files from subdirectories into a single file using simple `Bash` commands. Optimize your workflow by avoiding unnecessary file copies.
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This video is based on the question https://stackoverflow.com/q/73347960/ asked by the user 'statlerNwaldorf' ( https://stackoverflow.com/u/18521201/ ) and on the answer https://stackoverflow.com/a/73351823/ provided by the user 'M. Nejat Aydin' ( https://stackoverflow.com/u/13809001/ ) 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: Concatenating many text files based on intermediate directory names
Also, Content (except music) licensed under CC BY-SA https://meta.stackexchange.com/help/licensing
The original Question post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/by-sa/4.0/ ) license, and the original Answer post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/by-sa/4.0/ ) license.
If anything seems off to you, please feel free to write me at vlogize [AT] gmail [DOT] com.
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Concatenating Text Files in Nested Directories with Bash
Have you ever faced the challenge of merging text files scattered across multiple subdirectories? Perhaps you are dealing with bioinformatics data, like FASTA files, organized in a hierarchical structure that makes this task cumbersome. In this post, we will explore an efficient solution using Bash that not only simplifies the concatenation process but also avoids unnecessary duplication of data.
The Problem
In many projects, especially in fields like bioinformatics, files can be organized into subdirectories. If you want to concatenate contents of specific files from various locations, it often requires either moving files into a single folder or executing complex scripts. Here’s a typical directory structure you might encounter:
[[See Video to Reveal this Text or Code Snippet]]
From this structure, you may want to create a new concatenated file for each unique identifier (like “1234”) that merges content from its respective files across different directories.
The Solution
To solve this problem, we can use a simple Bash script that iterates through the files, creates necessary directories, and concatenates the contents without copying files to a temporary location. Here’s how to do it:
Step-by-Step Guide
Navigate to Your Project Directory:
Make sure you’re in the main directory (my_project).
[[See Video to Reveal this Text or Code Snippet]]
Run the Following Script:
This script will:
Look for all files matching the *_contigs.fasta pattern.
Create the appropriate directory in concats.
Concatenate the file contents into a new file.
[[See Video to Reveal this Text or Code Snippet]]
Explanation of the Script Components
Identifying Files: The for src in */*/*_contigs.fasta; statement identifies all files that match the naming convention you are interested in.
Directory Creation: The mkdir -p "concats/$dir" command makes sure that the necessary directories for the concatenated files are created without overwriting any existing ones.
Concatenation: The cat "$src" >> "concats/$dir/${file/contigs/concat}" line appends the content of current file ($src) into the new concatenated file, which is named by replacing _contigs in the original filename with _concat.
Result
Running this script generates a new directory structure under concats, organized by the identifiers:
[[See Video to Reveal this Text or Code Snippet]]
This approach prevents unnecessary copying of files and simplifies your workflow significantly.
Conclusion
By applying this Bash solution, you can effectively concatenate files distributed across various subdirectories without any hassle. This not only optimizes your file management process but also enhances your productivity when dealing with large datasets.
Try implementing this script in your projects and experience the efficiency it brings to file handling!
Видео Concatenating Text Files in Nested Directories with Bash канала vlogize
---
This video is based on the question https://stackoverflow.com/q/73347960/ asked by the user 'statlerNwaldorf' ( https://stackoverflow.com/u/18521201/ ) and on the answer https://stackoverflow.com/a/73351823/ provided by the user 'M. Nejat Aydin' ( https://stackoverflow.com/u/13809001/ ) 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: Concatenating many text files based on intermediate directory names
Also, Content (except music) licensed under CC BY-SA https://meta.stackexchange.com/help/licensing
The original Question post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/by-sa/4.0/ ) license, and the original Answer post is licensed under the 'CC BY-SA 4.0' ( https://creativecommons.org/licenses/by-sa/4.0/ ) license.
If anything seems off to you, please feel free to write me at vlogize [AT] gmail [DOT] com.
---
Concatenating Text Files in Nested Directories with Bash
Have you ever faced the challenge of merging text files scattered across multiple subdirectories? Perhaps you are dealing with bioinformatics data, like FASTA files, organized in a hierarchical structure that makes this task cumbersome. In this post, we will explore an efficient solution using Bash that not only simplifies the concatenation process but also avoids unnecessary duplication of data.
The Problem
In many projects, especially in fields like bioinformatics, files can be organized into subdirectories. If you want to concatenate contents of specific files from various locations, it often requires either moving files into a single folder or executing complex scripts. Here’s a typical directory structure you might encounter:
[[See Video to Reveal this Text or Code Snippet]]
From this structure, you may want to create a new concatenated file for each unique identifier (like “1234”) that merges content from its respective files across different directories.
The Solution
To solve this problem, we can use a simple Bash script that iterates through the files, creates necessary directories, and concatenates the contents without copying files to a temporary location. Here’s how to do it:
Step-by-Step Guide
Navigate to Your Project Directory:
Make sure you’re in the main directory (my_project).
[[See Video to Reveal this Text or Code Snippet]]
Run the Following Script:
This script will:
Look for all files matching the *_contigs.fasta pattern.
Create the appropriate directory in concats.
Concatenate the file contents into a new file.
[[See Video to Reveal this Text or Code Snippet]]
Explanation of the Script Components
Identifying Files: The for src in */*/*_contigs.fasta; statement identifies all files that match the naming convention you are interested in.
Directory Creation: The mkdir -p "concats/$dir" command makes sure that the necessary directories for the concatenated files are created without overwriting any existing ones.
Concatenation: The cat "$src" >> "concats/$dir/${file/contigs/concat}" line appends the content of current file ($src) into the new concatenated file, which is named by replacing _contigs in the original filename with _concat.
Result
Running this script generates a new directory structure under concats, organized by the identifiers:
[[See Video to Reveal this Text or Code Snippet]]
This approach prevents unnecessary copying of files and simplifies your workflow significantly.
Conclusion
By applying this Bash solution, you can effectively concatenate files distributed across various subdirectories without any hassle. This not only optimizes your file management process but also enhances your productivity when dealing with large datasets.
Try implementing this script in your projects and experience the efficiency it brings to file handling!
Видео Concatenating Text Files in Nested Directories with Bash канала vlogize
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