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
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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
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
@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
},
}
1 maintainer
Metadata
1 maintainer
Release files for bioat 0.17.5.post1
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| bioat-0.17.5.post1.tar.gz | 1.1 MB | Without provenance | Details for bioat-0.17.5.post1.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| bioat-0.17.5.post1-py3-none-any.whl | Python 3 | none | any | Details for bioat-0.17.5.post1-py3-none-any.whl |
Total release size: 2.2 MB
Release files / bioat-0.17.5.post1.tar.gz
| Download URL | bioat-0.17.5.post1.tar.gz |
|---|---|
| Size | 1.1 MB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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No |
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Release files / bioat-0.17.5.post1-py3-none-any.whl
| Download URL | bioat-0.17.5.post1-py3-none-any.whl |
|---|---|
| Size | 1.1 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
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uv/0.12.3 {"installer":{"name":"uv","version":"0.12.3","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"macOS","version":null,"id":null,"libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":null}
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Security for bioat 0.17.5.post1
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