westminster

Benchmarking baskerville models for regulatory sequence activity prediction

Installation

git clone git@github.com:calico/westminster.git cd westminster pip install .

To set up the required environment variables: cd westminster conda activate <conda_env> ./env_vars.sh

Note: Change the line of code at the top of './env_vars.sh' to your local path.

Alternatively, the environment variables can be set manually:

export WESTMINSTER_DIR=/home/<user_path>/westminster
export PATH=$WESTMINSTER_DIR/src/westminster/scripts:$PATH
export PYTHONPATH=$WESTMINSTER_DIR/src/westminster/scripts:$PYTHONPATH

Benchmark data

The fine-mapped GTEx QTL sets used by westminster_{eqtl,sqtl,paqtl}_folds.py are built and released by calico/qtl-bench. Fetch a release and point --vcf_dir at one of its set directories, e.g. data/gtex11/snp/eqtl.

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Contacts

Dave Kelley (codeowner)