Metadata-Version: 2.4
Name: jlsteenwyk-biokit
Version: 1.1.20
Home-page: https://github.com/jlsteenwyk/biokit
Author: Jacob L. Steenwyk
Author-email: jlsteenwyk@gmail.com
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: biopython>=1.82
Requires-Dist: matplotlib>=3.6.0
Requires-Dist: numpy>=1.24.0
Requires-Dist: cython
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: license-file
Dynamic: requires-dist
Dynamic: requires-python

<p align="center">
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  </a>
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    <a href="https://jlsteenwyk.com/BioKIT/">Docs</a>
    ·
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    ·
    <a href="https://github.com/jlsteenwyk/biokit/issues">Request Feature</a>
  </p>
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</p>

BioKIT is a UNIX shell toolkit for processing molecular sequence data.<br /><br />
If you found BioKIT useful, please cite the following: *BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data*. Genetics. doi: [10.1093/genetics/iyac079](https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyac079/6583183).
<br /><br />

---

This documentation covers downloading and installing BioKIT. Details about each function as well as tutorials for using BioKIT are available in the <a href="https://jlsteenwyk.com/BioKIT/">online documentation</a>.

<br />

**Installation** <br />

**If you are having trouble installing BioKIT, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**

To install using *pip*, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:
```shell
# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install biokit
pip install jlsteenwyk-biokit
```

**Note, the virtual environment must be activated to use biokit.**

After using biokit, you may wish to deactivate your virtual environment and can do so using the following command:
```shell
# deactivate virtual environment
deactivate
```

<br />

Similarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:
```shell
# download
git clone https://github.com/JLSteenwyk/BioKIT.git
cd BioKIT/
# create virtual environment
python -m venv .venv
# activate virtual environment
source .venv/bin/activate
# install
make install
```
To deactivate your virtual environment, use the following command:
```shell
# deactivate virtual environment
deactivate
```
**Note, the virtual environment must be activated to use biokit.**

<br />

To install via anaconda, execute the following command:
```shell
conda install -c jlsteenwyk jlsteenwyk-biokit
```
Visit here for more information:
https://anaconda.org/JLSteenwyk/jlsteenwyk-biokit

<br />

To test biokit installation, launch the help message

```shell
biokit -h
```

## Development

Common local quality checks and profiling workflows are documented in:

- `docs/dev/developer_workflow.rst`
