abutils

Models, functions and visualization tools for working with adaptive immune receptore repertoire (AIRR) data. The primary purpose of abutils is to provide generalizable tools suitable for direct use analyzing bulk AIRR datasets, and is used by scab for single cell AIRR analysis. abutils is a core component of the ab[x] toolkit for AIRR data analysis.

Source code: github.com/briney/abutils
Documentation: abutils.readthedocs.org
Download: pypi.python.org/pypi/abutils
Docker: hub.docker.com/r/brineylab/datascience/

install

pip install abutils

api

We've tried to design the abutils API to be intuitive yet powerful, with the goal of enabling both interactive analyses (via environments like Jupyter notebooks) as well as integration of abutils tools into more complex analysis pipelines and/or standalone software tools. See the documentation for more detail about the API. As always, any feedback is greatly appreciated!!

testing

You can run the complete abutils test suite by first installing pytest:

pip install pytest

and then running:

git clone https://github.com/brineylab/abutils
cd abutils
pytest

This test suite is automatically run against all supported versions of Python following every commit.

requirements

python 3.10+

abstar
baltic
biopython
dnachisel
fastcluster
matplotlib
mnemonic
natsort
numpy
pandas
parasail
polars
prettytable
pyarrow
pyfamsa
pyfastx
pytest
python-circos
pyyaml
rapidfuzz
sample-sheet
scikit-learn
scipy
seaborn
smart_open
tqdm

abutils includes several additional binaries that are required for certain functionality:

abutils.tl.mafft uses MAFFT
abutils.tl.muscle uses MUSCLE
abutils.tl.cluster uses CD-HIT, MMseqs2, and VSEARCH
abutils.tl.fasttree uses FastTree

Although these binaries are all packaged into abutils, each respective abutils.tl function provides the option to supply a alternate binary path in case you'd prefer to use a different version.

Metadata

Release files for abutils 0.6.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for abutils 0.6.0
File	Size	Uploaded
abutils-0.6.0.tar.gz	86.1 MB	Apr 14, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for abutils 0.6.0
File	Interpreter	ABI	Platform	Reset
abutils-0.6.0-py3-none-any.whl 86.7 MB Apr 14, 2026	Python 3	none	any	Details

Total release size: 172.8 MB

Release files / abutils-0.6.0.tar.gz

Download URL	abutils-0.6.0.tar.gz
Size	86.1 MB
Tags	Source
SHA-256 checksum How to use checksums	`7907c07bfc5d133ffcf74e8b3d5536a197018c8a654143a160db5a484478c071`
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Upload date	Apr 14, 2026
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Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing platform: GitHub Actions
Publishing repository: github.com/brineylab/abutils
Publishing commit: github.com/brineylab/abutils/tree/f238674d077377a94239053a8725144ce8d21d6f

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Publishing configuration: github.com/brineylab/abutils/blob/f238674d077377a94239053a8725144ce8d21d6f/.github/workflows/pythonpublish.yml
Publishing logs: github.com/brineylab/abutils/actions/runs/24411255405/attempts/1

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SHA-256 checksum: 7907c07bfc5d133ffcf74e8b3d5536a197018c8a654143a160db5a484478c071 Verifying attestations

Release files / abutils-0.6.0-py3-none-any.whl

Download URL	abutils-0.6.0-py3-none-any.whl
Size	86.7 MB
Tags	Python 3
SHA-256 checksum How to use checksums	`3796a186ec1f9a3ff4de64328ef7ad0bf8cd838f70b49aa1f574a54c8a41351c`
BLAKE2b-256 checksum How to use checksums	`37cab39b2b08068fdee98e3f65749790dd367c08536ada07acb9ba2d5d386709`
Upload date	Apr 14, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/brineylab/abutils
Publishing commit: github.com/brineylab/abutils/tree/f238674d077377a94239053a8725144ce8d21d6f

Workflow

Publishing configuration: github.com/brineylab/abutils/blob/f238674d077377a94239053a8725144ce8d21d6f/.github/workflows/pythonpublish.yml
Publishing logs: github.com/brineylab/abutils/actions/runs/24411255405/attempts/1

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Subject: abutils-0.6.0-py3-none-any.whl
SHA-256 checksum: 3796a186ec1f9a3ff4de64328ef7ad0bf8cd838f70b49aa1f574a54c8a41351c Verifying attestations