Lesson 4 — Simple For Loops

Learning Objectives

By the end of this lesson, you will be able to:

• Explain what a for loop does and why it is useful
• Write a basic for loop in Bash
• Loop over a fixed list of values
• Loop over a set of files using a wildcard pattern (*.fastq)
• Combine loops with variables and basename

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1. Why Loops?

In Lesson 3, you wrote a script that processed one file. What if you have ten files? You could copy and paste the same commands ten times — but that defeats the purpose of scripting.

A for loop solves this. It lets you write a set of commands once and have Bash repeat them for each item in a list.

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2. The For Loop Structure

Here is the structure of a Bash for loop:

for VARIABLE in item1 item2 item3
do
    command using $VARIABLE
done

Breaking it down:

• for starts the loop
• VARIABLE is a name you choose — Bash will assign it each item from the list, one at a time
• in is followed by the list of items
• do marks the start of the commands to repeat
• done marks the end of the loop

Everything between do and done runs once for every item in the list.

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3. A Simple Example

Let us start with a small example before using real files:

#!/bin/bash

for SAMPLE in SRR001 SRR002 SRR003
do
    echo "Processing sample: $SAMPLE"
done

Output:

Processing sample: SRR001
Processing sample: SRR002
Processing sample: SRR003

What happened:

1. Bash assigned SRR001 to SAMPLE, then ran echo
2. Bash assigned SRR002 to SAMPLE, then ran echo
3. Bash assigned SRR003 to SAMPLE, then ran echo
4. The list was exhausted — the loop ended

The commands between do and done can be anything: echo, fastqc, cp, mv — as many commands as you need.

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4. Looping Over Files

Typing out every sample name by hand is still repetitive. Instead, you can use a wildcard pattern to match files automatically.

The * character matches any sequence of characters. So:

*.fastq

means “every file whose name ends in .fastq.”

Here is a loop that prints the name of every FASTQ file in the paired reads folder:

#!/bin/bash

for FILE in Training/short_reads/paired/*.fastq
do
    echo $FILE
done

Output:

Training/short_reads/paired/SRR1553607_1.fastq
Training/short_reads/paired/SRR1553607_2.fastq

Bash expanded *.fastq into the list of matching files and looped over each one automatically. If you add more .fastq files to that folder, the loop will include them the next time you run the script — without any changes to the script itself.

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5. Combining Loops with basename

Now combine what you learned in Lesson 3 with a loop. Inside the loop, use basename to get the clean sample name from each file path:

#!/bin/bash

for FILE in Training/short_reads/paired/*.fastq
do
    SAMPLE=$(basename $FILE .fastq)
    echo "Sample: $SAMPLE"
    echo "File:   $FILE"
done

Output:

Sample: SRR1553607_1
File:   Training/short_reads/paired/SRR1553607_1.fastq
Sample: SRR1553607_2
File:   Training/short_reads/paired/SRR1553607_2.fastq

On each pass through the loop:

• $FILE holds the full path to one FASTQ file
• $SAMPLE holds the clean name extracted from that path
• Both are available to use in any command inside the loop

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6. Running FastQC in a Loop

Here is a loop that does real work — running FastQC on every FASTQ file in the folder:

#!/bin/bash

for FILE in Training/short_reads/paired/*.fastq
do
    SAMPLE=$(basename $FILE .fastq)
    echo "Running FastQC on: $SAMPLE"
    fastqc $FILE
done

Save this as loop_fastqc.sh, make it executable, and run it:

chmod +x loop_fastqc.sh
./loop_fastqc.sh

FastQC will run on each .fastq file in turn. This script already does everything the manual approach did — but in a form that scales to any number of files.

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Summary

• A for loop repeats commands for each item in a list
• The loop variable (FILE, SAMPLE, etc.) takes a new value on each pass through the loop
• *.fastq matches all files ending in .fastq at the specified path
• basename can be used inside a loop to extract a clean sample name from each file path
• Adding new files to the folder automatically includes them in future runs — no script changes needed

In the final lesson, you will combine everything — shebang, variables, basename, and a loop — into a complete, well-structured script ready for real use.