Mutate Multi-FASTA

Introduction

This program is designed to mutate a multi-FASTA file. It takes as input an FASTA (gzip) file and a BED file specifying the regions to be mutated.

Input Files

1. influenza.fna.gz: This file contains the original multi-FASTA sequence of the influenza virus. To download this file, please visit the NCBI link.

2. bed_file.bed: This BED file contains the regions to be mutated in the FASTA file. It should be available in the current working directory.

   Note: The input FASTA file is provided in gzip format for convenience. The original FASTA file is approximately ~1.3 GB in size, which may be cumbersome to download and upload. Therefore, a gzip file is used as input here.

Make sure these files are present in your current working directory before running the program.

How to Use

1. Download Input Files:

   • Download the influenza.fna.gz file from the provided NCBI link.
   • Ensure the bed_file.bed is available in your current working directory.

2. Run the main.py script:

   • Execute the main.py script.

3. View Output:

   • Once the program has completed execution, the mutated multi-FASTA file will be generated.
   • Output file name : mutated.fasta

Notes

• The program utilizes the BED file format to specify the regions for mutation.
• Mutation operations : Replacing the first occurrence of adenine (A) with cytosine (C) in the subsequence

Dependencies

• Python 3.x

Date of creation : 17 Feb 2024 | Developer : Vinit Gupta