🧬 FASTA File Analysis using Shell Scripting

📘 Project Description

This repository contains a comprehensive set of shell scripts for performing essential FASTA file operations in bioinformatics. It demonstrates how command-line tools and Bash scripting can automate sequence analysis — from calculating GC content to motif detection, filtering, and classification.

🧪 Key Sections

1️⃣ What is FASTA File Analysis?

FASTA files store biological sequence data (DNA, RNA, or protein). This project shows how to extract useful biological insights from these sequences using Unix/Linux shell scripting — without relying on heavy bioinformatics software.

2️⃣ Objectives of the Project

Automate reading and analysis of FASTA sequences

Use loops, conditionals, and case statements for decision-based outputs

Implement common genomic calculations (GC%, length, motifs, complements)

Separate, classify, and filter sequences efficiently

3️⃣ Part A – Basic FASTA Operations

Script Description

count_sequences.sh - Counts total number of sequences

sequence_lengths.sh - Calculates and prints each sequence length

longest_shortest.sh - Finds longest and shortest sequences

gc.sh - Computes GC percentage for each sequence

extract_seq.sh -Extracts sequences longer than 30 bp

count_motif.sh - Searches motifs (ATG, TATA, CGC) in sequences

4️⃣ Part B – Loops & Conditionals in FASTA Analysis

Script Description

seq_length_classification.sh - Classifies sequences as Short, Medium, or Long

search1.sh - Loops through motifs and checks their presence

rev_comp_gc.sh - Prints reverse complement if GC% > 50

save_seq.sh - Saves long and short sequences separately

seq_filtering.sh - Filters sequences by user-defined minimum length

poly_a.sh - Detects poly(A) tails (AAA...) at sequence ends

count_nucleotides.sh Counts A, T, G, C nucleotides

palindromic.sh - Detects palindromic sequences

selected_genes.sh - Extracts specific Gene IDs (e.g., Gene1, Gene4)

gc_case.sh - Categorizes GC% using case statements (Low, Medium, High)

5️⃣ Input Files Used

File Description

all_sequences.fasta - Combined FASTA file containing multiple gene sequences

motifs.txt - Contains motifs to be searched (e.g., ATG, TATA, CGC)

⚙️ Usage Example

Make scripts executable

chmod +x *.sh

Run any script

./count_sequences.sh all_sequences.fasta

Example : search for motifs

./count_motif.sh TATA

🧰 Tools & Commands Used Category Commands / Concepts

Sequence processing grep, awk, wc, tr, rev Looping & conditions for, if, elif, case File handling Redirection (>, >>), conditional writes GC and motif analysis String pattern matching and arithmetic operations

📊 Learning Outcomes

Understand FASTA format and its biological relevance

Automate repetitive bioinformatics tasks using Bash

Gain hands-on experience in scripting logic and text parsing

Perform genomic feature analysis without external software

📄 Project Report You can view the complete project report here: https://github.com/DEBOPRIYA2320/FASTA-File-Analysis-using-Shell-Scripting/blob/747e866754b494d7bd6c3dacde0cecdd781178fa/Bash%20Scripting(GITHUB).pdf

🧠 Author Debopriya
📧 debopriya0920@gmail.com
🔗 GitHub
🔗 LinkedIn

🪪 License This work is licensed under the MIT License.

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