BAKIR - Biologically-informed Killer cell immunoglobulin-like receptor (KIR) gene annotation tool 🧬

bakir is a Python tool for gene sequence analysis, specifically focusing on the KIR (Killer-cell Immunoglobulin-like Receptor) genes. It automates the process of aligning sequences, identifying genes, and annotating them with relevant information such as functional variants and closest matching alleles.

Features 🚀

• Sequence alignment and gene identification
• Variant calling and functional annotation
• Selection of best matching alleles through functional varaint identification
• Support for manual annotation fixes through YAML files
• Easy integration with CI/CD pipelines
• Comprehensive test suite with pytest

Installation 📦

Native Installation 🌿

Clone the repository and navigate into the project directory:

git clone https://github.com/yourgithub/bakir.git
cd bakir

Install the environment with conda:

conda env create -f bakir-env.yml
conda activate bakir

Install the package (preferably in a virtual environment):

pip install .

Using Docker 🐳

To run bakir using Docker, you first need to pull the Docker image from Docker Hub:

docker pull cdslsahinalp/kir-annotator:latest

After pulling the image, you can run bakir using:

docker run -v $(pwd):/data cdslsahinalp/kir-annotator:latest [-o /data/OUTPUT] /data/sequence.fasta

Replace $(pwd) with the absolute path to the directory containing your data files if you are not running the command from within the data directory. This command mounts your current directory ($(pwd)) to /data inside the container.

Using Singularity 🌀

For environments where Docker is not available, you can use Singularity to run the Docker image. First, pull the Docker image as a Singularity image:

singularity pull docker://cdslsahinalp/kir-annotator:latest

Then, run bakir using the Singularity image:

singularity exec --bind /path/to/data:/data kir-annotator_latest.sif bakir [-o /data/OUTPUT] /data/sequence.fasta

As with Docker, replace $(pwd) with the absolute path to your data directory if necessary. This command binds your current directory to /data inside the Singularity container.

Usage 🛠

To use bakir, you need to provide the path to your assembly sequence file and the gene database file at a minimum. Additional options allow for customization of the output and other functionalities:

usage: bakir [-h] [-d DATABASE] [-o OUTPUT] [-m MAPPING_CACHE] [-t TEMP_DIR] [-f FIXES] sequence

BAKIR: Biologically-informed Killer cell immunoglobulin-like receptor (KIR) gene annotation tool.

positional arguments:
  sequence              Path to the assembly sequence file.

optional arguments:
  -h, --help            show this help message and exit
  -d DATABASE, --database DATABASE
                        Path to the gene database file.
  -o OUTPUT, --output OUTPUT
                        Optional: Path and prefix for the output file. If not provided, a default name based on the sequence file name will be used.
  -m MAPPING_CACHE, --mapping_cache MAPPING_CACHE
                        Optional: Path for the mapping cache file. If not provided, mapping results will not be cached.
  -t TEMP_DIR, --temp_dir TEMP_DIR
                        Optional: Path for the temporary directory. If not provided, the system default temporary directory will be used.
  -f FIXES, --fixes FIXES
                        Optional: Path to the YAML file containing manual annotation fixes. If not provided, no manual fixes will be applied.

Development 🛠️

Testing

We use pytest for testing. To run the tests:

pytest tests/

CI/CD

This project is set up with CI/CD practices in mind. Automated tests are run on every push, ensuring code quality and functionality.

Contributing

Contributions are welcome! Please feel free to submit a pull request or open an issue.