Lesson 3 — Variables and basename

Learning Objectives

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

• Create a variable and assign it a value
• Use a variable in a command
• Store a file path in a variable
• Use the basename command to extract a filename from a full path
• Use $() to store the result of a command in a variable

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1. What Is a Variable?

A variable is a named container that holds a value. Instead of typing the same file path over and over throughout a script, you store it once in a variable and use the variable name everywhere else.

If the path ever changes, you update it in one place — not in every command throughout the script.

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2. Creating a Variable

In Bash, you create a variable by writing its name, an equals sign, and the value:

SAMPLE="SRR1553607"

Three important rules:

1. No spaces around the = sign. SAMPLE = "SRR1553607" will fail with an error.
2. Variable names are case-sensitive. SAMPLE and sample are two different variables.
3. Use uppercase names for variables in scripts. This is a convention that makes scripts easier to read — it helps you instantly see what is a variable and what is a command.

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3. Using a Variable

To use the value stored in a variable, put a $ in front of its name:

SAMPLE="SRR1553607"
echo $SAMPLE

Output:

SRR1553607

You can use a variable anywhere you would type the value directly:

INPUT="Training/short_reads/paired/SRR1553607_1.fastq"
fastqc $INPUT

This is exactly the same as typing fastqc Training/short_reads/paired/SRR1553607_1.fastq — but now the path is stored once, at the top of the script, where it is easy to find and change.

You can also mix variables with other text inside echo:

echo "Running FastQC on: $INPUT"

Output:

Running FastQC on: Training/short_reads/paired/SRR1553607_1.fastq

Bash replaces $INPUT with its value before printing.

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4. Storing a File Path in a Variable

Here is a practical example. Create a new script:

nano qc_one_sample.sh

Type the following:

#!/bin/bash

# Store the file path in a variable
INPUT="Training/short_reads/paired/SRR1553607_1.fastq"

# Use the variable to run FastQC
echo "Running FastQC on: $INPUT"
fastqc $INPUT

Save and make it executable:

chmod +x qc_one_sample.sh
./qc_one_sample.sh

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5. The basename Command

When working with file paths, you often need just the filename — without the directory path in front of it. The basename command does exactly this.

Try it directly in the terminal first:

basename Training/short_reads/paired/SRR1553607_1.fastq

Output:

SRR1553607_1.fastq

basename stripped away Training/short_reads/paired/ and left just the filename.

Removing the extension too

You can also tell basename to remove a specific extension by adding it as a second argument:

basename Training/short_reads/paired/SRR1553607_1.fastq .fastq

Output:

SRR1553607_1

This gives you the clean sample name — no directory path, no file extension. This is extremely useful for naming output files after their corresponding input files, or for printing meaningful progress messages.

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6. Storing a Command’s Result in a Variable

You can store the output of any command in a variable using $():

SAMPLE=$(basename Training/short_reads/paired/SRR1553607_1.fastq .fastq)
echo $SAMPLE

Output:

SRR1553607_1

The $() syntax is called command substitution. It tells Bash: run the command inside the brackets, and use whatever it prints as the value. The result is stored directly in the variable.

Here it is using a variable for the input path:

INPUT="Training/short_reads/paired/SRR1553607_1.fastq"
SAMPLE=$(basename $INPUT .fastq)

echo "Sample name: $SAMPLE"

Output:

Sample name: SRR1553607_1

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7. A Complete Example

Here is a script that brings all the variable concepts from this lesson together:

#!/bin/bash

# Define the input file
INPUT="Training/short_reads/paired/SRR1553607_1.fastq"

# Extract the sample name from the filename
SAMPLE=$(basename $INPUT .fastq)

# Print what we are about to do
echo "Processing sample: $SAMPLE"
echo "Input file: $INPUT"

# Run FastQC
fastqc $INPUT

Save this as qc_with_variables.sh, then run it:

chmod +x qc_with_variables.sh
./qc_with_variables.sh

Expected output:

Processing sample: SRR1553607_1
Input file: Training/short_reads/paired/SRR1553607_1.fastq

Followed by the FastQC output.

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Summary

• Variables store values so you can reuse them without retyping — define once, use everywhere
• Create a variable with NAME="value" — no spaces around =
• Use a variable with $NAME
• basename /path/to/file.fastq returns just file.fastq
• basename /path/to/file.fastq .fastq returns file with no extension
• $() runs a command and stores the result in a variable — this is command substitution

In the next lesson, you will use variables inside a loop to process multiple files automatically.