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Style][code-style-badge]][code-style-link]\n[![Type Checked][type-checking-badge]][type-checking-link]\n[![PEP8][pep-8-badge]][pep-8-link]\n[![Code Coverage][code-coverage-badge]][code-coverage-link]\n[![License][license-badge]][license-link]\n\n---\n\n[![Python package][python-package-badge]][python-package-link]\n[![PyPI version][pypi-badge]][pypi-link]\n[![PyPI download total][pypi-downloads-badge]][pypi-downloads-link]\n[![DOI][zenodo-badge]][zenodo-link]\n\n---\n\n[language-badge]:       http://img.shields.io/badge/language-python-brightgreen.svg\n[language-link]:        http://www.python.org/\n[code-style-badge]:     https://img.shields.io/badge/code%20style-black-000000.svg\n[code-style-link]:      https://black.readthedocs.io/en/stable/ \n[type-checking-badge]:  http://www.mypy-lang.org/static/mypy_badge.svg\n[type-checking-link]:   http://mypy-lang.org/\n[pep-8-badge]:          https://img.shields.io/badge/code%20style-pep8-brightgreen.svg\n[pep-8-link]:           https://www.python.org/dev/peps/pep-0008/\n[code-coverage-badge]:  https://codecov.io/gh/fulcrumgenomics/pybedlite/branch/main/graph/badge.svg\n[code-coverage-link]:   https://codecov.io/gh/fulcrumgenomics/pybedlite\n[license-badge]:        http://img.shields.io/badge/license-MIT-blue.svg\n[license-link]:         https://github.com/fulcrumgenomics/pybedlite/blob/main/LICENSE\n[python-package-badge]: https://github.com/fulcrumgenomics/pybedlite/workflows/Python%20package/badge.svg\n[python-package-link]:  https://github.com/fulcrumgenomics/pybedlite/actions?query=workflow%3A%22Python+package%22\n[pypi-badge]:           https://badge.fury.io/py/pybedlite.svg\n[pypi-link]:            https://pypi.python.org/pypi/pybedlite\n[pypi-downloads-badge]: https://img.shields.io/pypi/dm/pybedlite\n[pypi-downloads-link]:  https://pypi.python.org/pypi/pybedlite\n[zenodo-badge]:         https://zenodo.org/badge/442541029.svg\n[zenodo-link]:          https://doi.org/10.5281/zenodo.11223166\n\n# pybedlite\n\nLightweight Python interfaces for reading, writing, and querying Genomic Regions (BED).\n\n\u003cp\u003e\n\u003ca href=\"https://fulcrumgenomics.com\"\u003e\u003cimg src=\".github/logos/fulcrumgenomics.svg\" alt=\"Fulcrum Genomics\" height=\"100\"/\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n[Visit us at Fulcrum Genomics](https://www.fulcrumgenomics.com) to learn more about how we can power your Bioinformatics with pybedlite and beyond.\n\n\u003ca href=\"mailto:contact@fulcrumgenomics.com?subject=[GitHub inquiry]\"\u003e\u003cimg src=\"https://img.shields.io/badge/Email_us-brightgreen.svg?\u0026style=for-the-badge\u0026logo=gmail\u0026logoColor=white\"/\u003e\u003c/a\u003e\n\u003ca href=\"https://www.fulcrumgenomics.com\"\u003e\u003cimg src=\"https://img.shields.io/badge/Visit_Us-blue.svg?\u0026style=for-the-badge\u0026logo=wordpress\u0026logoColor=white\"/\u003e\u003c/a\u003e\n\nSee documentation on [pybedlite.readthedocs.org][rtd-link].\n\n```\npip install pybedlite\n```\nOR\n```\nconda install -c bioconda pybedlite\n```\nOR\n```\nconda create -n pybedlite pybedlite\nconda activate pybedlite\n```\n\n[rtd-link]:    http://pybedlite.readthedocs.org/en/stable\n\n**Requires python 3.9+** \n\n# Getting Setup for Development Work\n\nClone the repository to your local machine. Note that pybedlite \u003e= 0.0.4 includes [cgranges][cgranges-link] as a submodule, so you must use the `--recurse-submodules` option:\n```\ngit clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git\n```\n\n[Poetry][poetry-link] is used to manage the python development environment.\n\nA simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link].  E.g.:\n\n```bash\nconda create -n pybedlite python=3.9 poetry\nconda activate pybedlite\npoetry install\n```\n\nIf the methods listed above do not work try the following:\n```bash\nmamba create -n pybedlite -c conda-forge \"python=3.9.16\" \"poetry=1.6.1\"\nmamba activate pybedlite\npoetry install\n```\n\nIf, during `poetry install` on Mac OS X errors are encountered running gcc/clang to build `pybedtools` or other packages with native code, try setting the following and re-running `poetry install`:\n```bash\nexport CFLAGS=\"-stdlib=libc++\"\n``` \n\n[poetry-link]: https://github.com/python-poetry/poetry\n[conda-link]:  https://docs.conda.io/en/latest/miniconda.html\n[cgranges-link]: https://github.com/lh3/cgranges\n\n## Checking the Build\n### Run all checks with:\n```bash\n./ci/check.sh\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffulcrumgenomics%2Fpybedlite","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ffulcrumgenomics%2Fpybedlite","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ffulcrumgenomics%2Fpybedlite/lists"}