Introduction to Bash Scripting for Biology

What is Bash Scripting?

Bash scripting is like writing a recipe for your computer - it's a series of commands that:

Automates repetitive tasks
Processes files and data
Combines multiple commands

1. Script Components Explained

        #!/bin/bash  # Shebang line

        # This is a comment # Explanatory text

        echo "Analyzing DNA sequences"  # Command

Key Elements of a Bash Script

Shebang Line (#!): First line starting with #!
- Tells the computer this is a Bash script
- Always use: #!/bin/bash

Comments: Lines starting with #
- Ignored by the computer
- Help explain your code

Commands: Instructions to execute
- Same commands you'd type in terminal
- Example: echo, grep, wc

2. Creating a Basic Analysis Script

        #!/bin/bash

        # Create sample DNA file

        echo ">Sample1

        ATGCGATCG

        >Sample2

        TAGCTAGCTAG" > sequences.fasta

        # Count sequences

        echo "Number of sequences: $(grep -c '^>' sequences.fasta)"

        # Calculate total length

        total_length=$(grep -v '^>' sequences.fasta | tr -d '\n' | wc -c)

        echo "Total length: $total_length bp"

        # Calculate GC%

        gc_count=$(grep -v '^>' sequences.fasta | tr -d '\n' | tr -cd 'GC' | wc -c)

        gc_percent=$(echo "scale=2; ($gc_count/$total_length)*100" | bc)

        echo "GC Content: $gc_percent%"

Step-by-Step Explanation

Creating FASTA File:
- echo writes lines to sequences.fasta
- > indicates sequence names

Counting Sequences:
- grep -c '^>' counts lines starting with >

Calculating Length:
1. grep -v '^>': Exclude header lines
2. tr -d '\n': Remove line breaks
3. wc -c: Count characters

GC% Calculation:
1. tr -cd 'GC': Keep only G/C
2. bc: Calculator for percentage

3. Running Your Script

Execution Instructions

Save as dna_analysis.sh
Make executable:
chmod +x dna_analysis.sh
Run:
./dna_analysis.sh

4. Expected Output

        Number of sequences: 2

        Total length: 19 bp

        GC Content: 47.36%

Key Bash Concepts Used

Concept	Example	Purpose
Variables	total_length=...	Store values
Command Substitution	$(...)	Capture command output
Pipes (\|)	cmd1 \| cmd2	Pass output between commands
Redirection (> )	echo ... > file	Write to file

Why This Matters for Biology

Automate DNA sequence analysis
Process multiple files quickly
Reproduce analyses exactly
Handle large datasets efficiently