How to Map Columns from Two Files with Comma-Separated Values using awk

Описание: A comprehensive guide on using `awk` to map columns from two files, especially focusing on handling fifth columns with comma-separated characters.
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Mapping Columns from Two Files in awk

One common task in data processing is mapping columns from one file to columns in another file, especially when dealing with genetic data where specific identifiers and values are involved. If you have faced the challenge of matching columns from two files, let’s dive into a solution using the awk programming language—particularly focusing on cases where the columns may contain complex comma-separated data, such as genetic identifiers.

The Problem

In our scenario, we have two files (file1 and file2) that contain genomic information. Both files have a similar structure but differ in some values. Your goal is to match the first, second, and fourth columns of both files, while also carefully handling the fifth column, which contains comma-separated values with varying orders.

Example Input

File 1 (file1):

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

File 2 (file2):

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

Desired Output

When we find matching rows based on the first, second, and fourth columns, the output should look like this:

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

In this output:

The matching character from file1 is suffixed with *.

The non-matching character from file1 is suffixed with !.

The Solution

Using awk, we can efficiently match and manipulate the data as intended. The following awk script performs the necessary operations:

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

Explanation of the awk Script

Let’s break down this script step by step:

Data Storage:

The line FNR==NR { arr1[$1,$2,$4] = $5; next } checks if the first file (file1) is being read. It creates an associative array arr1, where keys are based on the first, second, and fourth columns, and values are from the fifth column.

Initialization:

The next block initializes the val variable and clears any previous arrays to prepare for new calculations.

Splitting Values:

The script uses split to separate the fifth column values from file1 into the arr2 array and also processes the fifth column from file2.

Matching Logic:

The condition (($1, $2, $4) in arr1) checks if the current row matches one in arr1. If it does, the script compares the corresponding fifth column values.

For each value in the fifth column, it checks if it exists in the previously stored arr4 and appends appropriate symbols (* or !) to the val variable accordingly.

Final Assembly:

After processing each line, it prepares the updated values to be printed, ensuring all unmatched values from file1 are also included.

Output:

Finally, 1 is a shorthand for printing the line, either modified or unmodified.

Conclusion

This awk script is a powerful solution for mapping columns between two files, especially when complex comma-separated values are involved. By following these steps, you can efficiently match genetic data and manipulate it according to your needs.

Feel free to adapt the script for your specific requirements, and happy data processing!