https://github.com/fulcrumgenomics/pybedlite
Lightweight Python interfaces for reading, writing, and querying Genomic Regions (BED)
https://github.com/fulcrumgenomics/pybedlite
bed-files bioinformatics genomics python
Last synced: 11 months ago
JSON representation
Lightweight Python interfaces for reading, writing, and querying Genomic Regions (BED)
- Host: GitHub
- URL: https://github.com/fulcrumgenomics/pybedlite
- Owner: fulcrumgenomics
- License: other
- Created: 2021-12-28T17:47:53.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2025-06-17T14:09:56.000Z (about 1 year ago)
- Last Synced: 2025-06-17T15:20:04.615Z (about 1 year ago)
- Topics: bed-files, bioinformatics, genomics, python
- Language: Python
- Homepage: https://pybedlite.readthedocs.io/en/latest/
- Size: 194 KB
- Stars: 14
- Watchers: 9
- Forks: 0
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: .github/CODEOWNERS
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# pybedlite
Lightweight Python interfaces for reading, writing, and querying Genomic Regions (BED).
[Visit us at Fulcrum Genomics](https://www.fulcrumgenomics.com) to learn more about how we can power your Bioinformatics with pybedlite and beyond.
See documentation on [pybedlite.readthedocs.org][rtd-link].
```
pip install pybedlite
```
OR
```
conda install -c bioconda pybedlite
```
OR
```
conda create -n pybedlite pybedlite
conda activate pybedlite
```
[rtd-link]: http://pybedlite.readthedocs.org/en/stable
**Requires python 3.9+**
# Getting Setup for Development Work
Clone the repository to your local machine. Note that pybedlite >= 0.0.4 includes [cgranges][cgranges-link] as a submodule, so you must use the `--recurse-submodules` option:
```
git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git
```
[Poetry][poetry-link] is used to manage the python development environment.
A simple way to create an environment with the desired version of python and poetry is to use [conda][conda-link]. E.g.:
```bash
conda create -n pybedlite python=3.9 poetry
conda activate pybedlite
poetry install
```
If the methods listed above do not work try the following:
```bash
mamba create -n pybedlite -c conda-forge "python=3.9.16" "poetry=1.6.1"
mamba activate pybedlite
poetry install
```
If, 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`:
```bash
export CFLAGS="-stdlib=libc++"
```
[poetry-link]: https://github.com/python-poetry/poetry
[conda-link]: https://docs.conda.io/en/latest/miniconda.html
[cgranges-link]: https://github.com/lh3/cgranges
## Checking the Build
### Run all checks with:
```bash
./ci/check.sh
```