Metadata-Version: 2.3
Name: prymer
Version: 3.0.0
Summary: Python primer design library
License: MIT
Keywords: bioinformatics,genomics,dna
Author: Yossi Farjoun
Author-email: yossi@fulcrumgenomics.com
Requires-Python: >=3.11,<4.0
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Documentation
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Dist: fgpyo (>=0.8.0,<0.9.0)
Requires-Dist: ordered-set (>=4.1.0,<5.0.0)
Requires-Dist: pybedlite (>=1.0.0,<2.0.0)
Requires-Dist: pyproject_hooks (>=1.0.0,<2.0.0,!=1.1.0)
Requires-Dist: pysam (>=0.22.1,<0.23.0)
Requires-Dist: strenum (>=0.4.15,<0.5.0)
Project-URL: Bug Tracker, https://github.com/fulcrumgenomics/prymer/issues
Project-URL: Documentation, https://github.com/fulcrumgenomics/prymer
Project-URL: Homepage, https://github.com/fulcrumgenomics/prymer
Project-URL: Repository, https://github.com/fulcrumgenomics/prymer
Description-Content-Type: text/markdown

# Python Primer Design Library

[![Python Versions][language-badge]][language-link]
[![License][license-badge]][license-link]
[![MyPy Checked][type-checking-badge]][type-checking-link]
[![Poetry][poetry-badge]][poetry-link]
[![Ruff][ruff-badge]][ruff-link]

[language-badge]:       https://img.shields.io/badge/python-3.11_|_3.12-blue
[language-link]:        http://www.python.org/
[license-badge]:        http://img.shields.io/badge/license-MIT-blue.svg
[license-link]:         https://github.com/fulcrumgenomics/prymer/blob/main/LICENSE
[type-checking-badge]:  http://www.mypy-lang.org/static/mypy_badge.svg
[type-checking-link]:   http://mypy-lang.org/
[poetry-badge]:         https://img.shields.io/endpoint?url=https://python-poetry.org/badge/v0.json
[poetry-link]:          https://python-poetry.org/
[ruff-badge]:           https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
[ruff-link]:            https://docs.astral.sh/ruff/

[![Install with Bioconda][bioconda-badge]][bioconda-link]
[![PyPI version][pypi-badge]][pypi-link]

[bioconda-badge]:       https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?label=Install%20with
[bioconda-link]:        http://bioconda.github.io/recipes/prymer/README.html
[pypi-badge]:           https://img.shields.io/pypi/v/prymer?label=Install%20with%20PyPi
[pypi-link]:            https://pypi.python.org/pypi/prymer

[![Bioconda][bioconda-dl-badge]][bioconda-dl-link]
[![PyPI download total][pypi-downloads-badge]][pypi-downloads-link]


[bioconda-dl-badge]:    https://img.shields.io/conda/dn/bioconda/prymer.svg?label=Bioconda%20downloads
[bioconda-dl-link]:     https://anaconda.org/bioconda/prymer
[pypi-downloads-badge]: https://img.shields.io/pypi/dm/prymer.svg?label=PyPi%20downloads
[pypi-downloads-link]:  https://pypi.python.org/pypi/prymer

[![tests][python-tests-badge]][python-tests-link]
[![publish prymer][publish-prymer-badge]][publish-prymer-link]
[![Code Coverage][code-coverage-badge]][code-coverage-link]

[publish-prymer-badge]: https://github.com/fulcrumgenomics/prymer/actions/workflows/publish_prymer.yml/badge.svg
[publish-prymer-link]:  https://github.com/fulcrumgenomics/prymer/actions/workflows/publish_prymer.yml
[python-tests-badge]:   https://github.com/fulcrumgenomics/prymer/actions/workflows/tests.yml/badge.svg
[python-tests-link]:    https://github.com/fulcrumgenomics/prymer/actions/workflows/tests.yml
[code-coverage-badge]:  https://codecov.io/gh/fulcrumgenomics/prymer/branch/main/graph/badge.svg
[code-coverage-link]:   https://codecov.io/gh/fulcrumgenomics/prymer

## Recommended Installation

The package `prymer` requires installation of [Primer3](https://github.com/primer3-org/primer3) and [interactive `bwa`](https://github.com/fulcrumgenomics/bwa-aln-interactive).

To satisfy these requirements, it is recommended to install using [bioconda](https://bioconda.github.io/):

```console
mamba install -c bioconda prymer
```

## Development and Testing

See the [developer's instructions][developers-instructions-link] for more information.

[developers-instructions-link]: https://prymer.readthedocs.io/en/latest/installation-and-developers-documentation.html#installation-for-development

