README.md

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pybedlite

Lightweight Python interfaces for reading, writing, and querying Genomic Regions (BED).

Visit us at Fulcrum Genomics to learn more about how we can power your Bioinformatics with pybedlite and beyond.

See documentation on pybedlite.readthedocs.org.

pip install pybedlite

OR

conda install -c bioconda pybedlite

OR

conda create -n pybedlite pybedlite
conda activate pybedlite

Requires python 3.8+ (for python < 3.8, please use pybedlite <= 0.0.3)

Getting Setup for Development Work

Clone the repository to your local machine. Note that pybedlite >= 0.0.4 includes cgranges as a submodule, so you must use the --recurse-submodules option:

git clone --recurse-submodules https://github.com/fulcrumgenomics/pybedlite.git

Poetry 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. E.g.:

conda create -n pybedlite python=3.8 poetry
conda activate pybedlite
poetry install

If the methods listed above do not work try the following:

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:

export CFLAGS="-stdlib=libc++"

Checking the Build

Run all checks with:

./ci/check.sh