BioSeeker

BioSeeker is a Python library and CLI tool for the analysis of codon and bicodon conservation rates across linked species.

This project facilitates calculating codon and bicodon conservation rates for a given genus. It is inspired by the paper Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection (Ghoneim et al., 2019).

Features

• Robust Parsing: Uses Biopython to handle standard FASTA/AFA formats.
• Efficient Analysis: Vectorized calculations using NumPy for performance.
• Conservation Metrics: Calculates conservation rates for both single codons and codon pairs (bicodons) across three reading frames (ORF 0, 1, 2).
• RSCU Analysis: Calculates Relative Synonymous Codon Usage (RSCU) for each species across the entire dataset.
• Aggregation: Automatically aggregates results from multiple alignment files.
• Dockerized: specific container for easy deployment and usage.

Installation

From Source

Requires Python 3.9+.

git clone https://github.com/SouthernBio/BioSeeker.git
cd BioSeeker
pip install .

Development

python3 -m venv venv
source venv/bin/activate
pip install -e .
pip install pytest

Usage

Command Line

BioSeeker provides a simple CLI. Place your aligned FASTA files (extension .afa, .fasta, or .fa) in a directory (e.g., FASTA_files).

bioseeker --input FASTA_files --output results

Arguments:

• --input, -i: Directory containing input alignment files (default: FASTA_files).
• --output, -o: Directory to save CSV results (default: results).

RSCU Analysis

To calculate the global RSCU values:

python src/bioseeker/analysis/rscu_analysis.py FASTA_files results/global_rscu.csv

Docker

You can run BioSeeker without installing Python dependencies using Docker.

Build the image:

docker build -t bioseeker .

Run the container: Assuming your data is in the current directory under FASTA_files:

docker run -v $(pwd)/FASTA_files:/data/input -v $(pwd)/results:/data/output bioseeker --input /data/input --output /data/output

Output

The tool generates CSV files in the output directory:

• codon_conservation_ORF0.csv, ORF1.csv, ORF2.csv
• bicodon_conservation_ORF0.csv, ORF1.csv, ORF2.csv

Each file contains:

• codon / codon_pair: The sequence.
• ReferenceCount: Occurrences in the reference sequence.
• ConservationCount: Number of times the codon was conserved (>90% match) across alignments.
• ConservationRate: ConservationCount / ReferenceCount.

License

GNU General Public License v3.0. See LICENSE.

💙 Support this project

Your contribution would help SouthernBio in improving the quality of this project and adding additional features. If you find this project useful and/or interesting, please consider offering your support on Github Sponsors, Ko-Fi or PayPal