BioAT

the Bioinformatic Analysis Tools

About bioat

Bref: bioat, a python package & command line toolkit for Bioinformatics and data science!

Home: https://github.com/hermanzhaozzzz/bioat

License: Apache-2.0

Name Downloads Version Platforms Test
Conda Recipe Conda Downloads Conda Version Conda Platforms Azure Pipelines

About author

Name: 赵华男 | Huanan Herman Zhao | EMail: hermanzhaozzzz AT gmail.com | Zhihu | BLOG

Installation

# supported platform: Linux / MacOS (intel & arm64) / Windows
pip install --upgrade bioat
# use conda
conda install -c conda-forge bioat

Usage

# list commands
bioat list
# check version
bioat version
# check information about bioat
bioat about

# example usage
bioat bam remove_clip --help
samtools view -h test_sorted_n.bam | bioat bam remove_clip | tail

circos plot

Development

# create/update .venv from pyproject.toml and uv.lock
uv sync

# run checks in the locked project environment
uv run pytest

# build distributions for release
uv build --no-sources --clear

Doc

See Doc

Citation

DOI

@software{huanan_herman_zhao_2025_15093444,
  author       = {Huanan Herman Zhao},
  title        = {BioAT, a python package \& command line toolkit for
                   bioinformatics and data science
                  },
  month        = mar,
  year         = 2025,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.15093444},
  url          = {https://doi.org/10.5281/zenodo.15093444},
  swhid        = {swh:1:dir:19b60f4b0b93f490798727c05ab41a3222b555a1
                   ;origin=https://doi.org/10.5281/zenodo.15093443;vi
                   sit=swh:1:snp:793130e9e84df8cf427ab2b6a69c0dc77146
                   1e6a;anchor=swh:1:rel:dc0fa360dfdaf99222cf7db99e8e
                   e9e898ac1c64;path=hermanzhaozzzz-bioat-4b611f2
                  },
}

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for hermanzhaozzzz from gravatar.com hermanzhaozzzz

Credits

PyPI data
Data sourced directly from PyPI's database.

Author/Maintainer: Huanan Herman Zhao

License expression

Apache-2.0
View SPDX License List

Requires

Python <4.0, >=3.10.0

Tags

bioat bioinformatics data science deep learning

Classifiers

Report project as malware

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Release history Release notifications | RSS feed

This release

0.17.5.post1 This release

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