Metadata-Version: 2.4
Name: cogent3_pykmertools
Version: 0.2.2
Summary: A cogent3 pykmertools app
Author-email: Anuradha Wickramarachchi <anuradhawick@gmail.com>
Requires-Python: >=3.11,<3.14
Description-Content-Type: text/markdown
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
License-File: LICENSE
Requires-Dist: cogent3>=2025.9.8a4
Requires-Dist: pykmertools>=0.2.1
Requires-Dist: ruff ; extra == "dev"
Requires-Dist: cogent3_pykmertools[test] ; extra == "dev"
Requires-Dist: pytest ; extra == "test"
Requires-Dist: pytest-cov ; extra == "test"
Requires-Dist: nox ; extra == "test"
Provides-Extra: dev
Provides-Extra: test

# `cogent3_pykmertools`: kmer counting plugins for `cogent3`

## Installation

We recommend installing `cogent3_pykmertools` from PyPI as follows

```
pip install cogent3_pykmertools
```

Or using `uv`

```
uv pip install cogent3_pykmertools
```

The installation process registers the apps and plugins with `cogent3`.

## The provided apps

- `pkt_count_kmers()`: does what the name says! When this package is installed, this app will be used by the `cogent3` `Sequence.count_kmers()` and `SequenceCollection.count_kmers()` methods. This app can also be run in parallel, which can be useful if you have a lot of sequences in the `SequenceCollection`.
- `pkt_kmer_header`: returns the k-mers as strings, so you know what their order is.

## Getting help on the apps

Use the `cogent3.app_help()` function. For example, `cogent3.app_help("pkt_count_kmers")`.

