Metadata-Version: 2.1
Name: bioat
Version: 0.4.2
Summary: Bioinformatic toolkit with python (It's still under development!)
Home-page: https://github.com/hermanzhaozzzz/BioinformaticAnalysisTools
License: MIT
Author: Herman Zhao
Author-email: hermanzhaozzzz@gmail.com
Requires-Python: >=3.9.0,<3.11
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Dist: biopython (>=1.80)
Requires-Dist: bs4 (>=0.0.1,<0.0.2)
Requires-Dist: cython (>=0.29.33)
Requires-Dist: fire (>=0.5.0)
Requires-Dist: ipython (>=8.14.0)
Requires-Dist: matplotlib (>=3.7.1)
Requires-Dist: numpy (>=1.24.1)
Requires-Dist: pandarallel (>=1.6.4)
Requires-Dist: pandas (>=1.5)
Requires-Dist: pysam (>=0.20.0)
Requires-Dist: recommonmark (>=0.7.1,<0.8.0)
Requires-Dist: requests (>=2.31.0,<3.0.0)
Requires-Dist: scipy (>=1.8.0)
Requires-Dist: selenium (>=4.11.2,<5.0.0)
Requires-Dist: sphinx (>=7.1.2,<8.0.0)
Requires-Dist: sphinx-autobuild (>=2021.3.14,<2022.0.0)
Requires-Dist: sphinx-markdown-tables (>=0.0.17,<0.0.18)
Requires-Dist: sphinx-rtd-theme (>=1.2.2,<2.0.0)
Requires-Dist: sphinxemoji (>=0.2.0,<0.3.0)
Requires-Dist: statsmodels (>=0.13.5)
Requires-Dist: tabulate (>=0.9.0)
Requires-Dist: tqdm (>=4.64.1)
Project-URL: Repository, https://github.com/hermanzhaozzzz/BioinformaticAnalysisTools
Description-Content-Type: text/markdown

# bioat 
the Bioinformatic Analysis Tools

![macos](https://github.com/hermanzhaozzzz/bioat/actions/workflows/macos.yml/badge.svg)
![linux](https://github.com/hermanzhaozzzz/bioat/actions/workflows/linux.yml/badge.svg)
![windows](https://github.com/hermanzhaozzzz/bioat/actions/workflows/windows.yml/badge.svg)

## about author

> author: [赵华男 | ZHAO Hua-nan](https://scholar.google.com/citations?user=ojSVoWQAAAAJ&hl=en)
>
> email: hermanzhaozzzz@gmail.com
>
> [Zhihu](https://www.zhihu.com/people/hymanzhaozzzz) | [BLOG](http://zhaohuanan.cc)

## Introduction
A python **package** & **command line toolkit** for Bioinformatics and data science!

**\<under development\>!!**

## Installation
```shell
# supported platform: Linux / MacOS (intel & arm64) / WSL on Windows
pip install --upgrade bioat
```


## usage
```shell
# 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](docs/demo_circos-plot.ipynb)

## known trouble
- sometimes, pysam dependent foo.lib can be absent, just `brew install foo.lib` to fix it.

