CoV2Mut

This is a Python script for generating SARS-CoV-2 spike protein sequences with specified mutations, given a reference sequence and a list of variants of interest.

Spike Variant Generator

About

CoV2Mut is a Python script specifically designed for generating spike protein sequences of SARS-CoV-2, including user-specified mutations. Given a reference sequence and a list of variants of interest, CoV2Mut enables researchers to simulate mutated SARS-CoV-2 sequences, contributing to ongoing research in the field of viral genomics and the study of COVID-19.

Installation

Clone this repository to your local machine using the following command:

git clone https://github.com/Paururo/CoV2Mut.git

Dependencies

CoV2Mut depends on the following Python packages:

Biopython
pandas
argparse
os
logging

Before running the script, please ensure these packages are installed in your Python environment. You can install these packages using pip:

pip install biopython pandas argparse

Usage

To use CoV2Mut, run the following command from your terminal:

python spike_variant_generator.py -r /path/to/reference.fasta -v /path/to/variants_of_interest.txt -n output_name.fasta -g yes -s yes

In this command:

-r specifies the path to the reference sequence FASTA file.
-v specifies the path to the text file containing variants of interest.
-n specifies the output FASTA filename.
-g decides whether to remove gaps ("-") in the sequences ("yes" to remove, "no" to retain).
-s decides whether to split the output multi-FASTA file into individual FASTA files ("yes" to split, "no" to retain as single file).

Please replace the paths and filenames with the actual ones on your system.

Contributing

We welcome contributions to CoV2SpikeMut! If you have a feature request, bug report, or proposal for improving the script, please open a new issue on GitHub issue tracker.

Contact

If you have any questions, comments, or would like to get in contact, please open an issue on GitHub issue tracker.