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Gene agnostic AlleleTools!

Working with alleles from highly polymorphic genes, like those in HLA and KIR clusters, is already hard enough! This repo is a collection of tools to facilitate your work on the manipulation and analysis of allele data sets.

The commands are sorted in three categories:

1. format: a group commands that convert allele data between different file formats. Including vcf, csv, our own format .alt (from allele table) and others.
2. plot: some commands to visualize allele data, specially from external sources.
3. test: perform statistical analysis on the allele dataset.

Warning

This project is currently under development in alpha stage. Some things might break. If that is the case, please do not hesitate to file an issue (clicking here)

Getting started

To install this package you can use pip:

pip install pip@git+https://github.com/nmendozam/alleleTools.git

It will install the altools command in your current environment. So, to execute a command you need to specify three things altools [tool_category] [tool_name] [input].

altools format from_vcf input.vcf

Other commands can be listed using:

altools --help
altools format --help

You can find more information about the usage in the documentation.

Cite

If you find this package useful for your research, please consider citing it. You can cite the current repository. Alternatively, although this is a personal project and has not been published yet, the first mention to the package was made in:

Mendoza-Mejía, N., Kolbe, D., Özer, O., Dose, J., Torres, G. G., Franke, A., Nygaard, M., & Nebel, A. (2025). HLA-DRB1*15:01 is associated with a reduced likelihood of longevity in northern European men. Genome Medicine, 17(1), 125. https://doi.org/10.1186/s13073-025-01554-1