HLA-PepClust

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Introduction

HLA-PepClust is a CLI tool designed for clustering peptide sequences based on their HLA binding motifs.

Prerequisites

Ensure your system meets the following requirements:

• Python 3.9 or higher
• pip (Python package manager)

Download or Clone the Repository

git clone https://github.com/Sanpme66/HLA-PepClust.git
cd HLA-PepClust/

Setting Up the Python Environment

1. Create a virtual environment

   python3 -m venv hlapepclust-env

2. Activate the virtual environment

   • macOS / Linux:

     source hlapepclust-env/bin/activate

   • Windows:

     .\hlapepclust-env\Scripts\activate

3. Upgrade pip

   pip install --upgrade pip

Installing Dependencies

1. Navigate to the project directory (if not already in it)

   cd HLA-PepClust/

2. Install the package and dependencies

   pip install -e .

Running HLA-PepClust

Display Help Message

To see available options and usage details:

clust-search -h      

Example of running the help clust-search -h command:

Command Structure

clust-search <input_data_path> <reference_data_path> \
  --hla_types <hla_types> \
  --n_clusters <number_of_clusters> \
  --output <output_path> \
  --species <Human or Mouse> \
  --threshold <similarity_threshold (default: 0.5)> \
  --log \
  --processes <number_of_threads>

Example Usage

clust-search data/D90_HLA_3844874 data/ref_data/Gibbs_motifs_human/output_matrices_human \
  --hla_types A0201,A0101,B1302,B3503,C0401 \
  --n_clusters 6 \
  --species human \
  --output test_results \
  --processes 4 \
  --threshold 0.6 

Command Line Arguments

Argument	Type	Description	Default
gibbs_folder	str	Path to test folder containing matrices.	Required
reference_folder	str	Path to reference folder containing matrices.	Required
-o, --output	str	Path to output folder.	"output"
-hla, --hla_types	list	List of HLA types to search.	All
-p, --processes	int	Number of parallel processes to use.	4
-n, --n_clusters	int	Number of clusters to search for.	"all"
-t, --threshold	float	Motif similarity threshold.	0.5
-s, --species	str	Species to search [Human, Mouse].	"human"
-db, --database	str	Generate a motif database from a configuration file.	"data/config.json"
-k, --best_KL	bool	Find the best KL divergence only.	False
-l, --log	bool	Enable logging.	False
-im, --immunolyser	bool	Enable immunolyser output.	False
-c, --credits	bool	Show credits for the motif database pipeline.	False
-v, --version	bool	Show the version of the pipeline.	False

Example Output

Example of running the clust-search command:

Deactivating the Virtual Environment

After finishing, deactivate the virtual environment with:

deactivate

Running HLA-PepClust in Google Colab

You can try out HLA-PepClust directly in Google Colab without installing anything on your local system!

Steps to Run in Colab

1. Click the "Open In Colab" button above.
2. Once the notebook opens in Colab, go to Runtime → Run All to execute all cells.
3. Modify input parameters if needed and run the pipeline in Colab.

Example of input folder path:

More detailed instructions coming soon... 🚀