CLI Reference

cli

cli

drexml CLI entry point.

cli [OPTIONS] COMMAND [ARGS]...

Options

--version: Show the version and exit.

explain

Explain how KDTs modulate a given disease map.

cli explain [OPTIONS] DISEASE_PATH

Options

--debug, --no-debug: Flag to run in debug mode.

--verbosity, --no-verbosity: Verbosity level.

--add, --no-add: Check the additivity when computing the SHAP values.

--n-iters <n_iters>: Number of Optimization iterations. 0 means use sensible hyperparameters.

--n-gpus <n_gpus>: Number of CUDA devices, -1 use all decices.

--n-cpus <n_cpus>: Number of CPUs, -1 use all decices.

--version: Show the version and exit.

Arguments

DISEASE_PATH: Required argument

orchestrate

Orchestrate the drexml procedure. Entry point for multi-disease workflows.

cli orchestrate [OPTIONS] DISEASE_PATH

Options

--debug, --no-debug: Flag to run in debug mode.

--verbosity, --no-verbosity: Verbosity level.

--version: Show the version and exit.

Arguments

DISEASE_PATH: Required argument

plot

Plot the stability results

cli plot [OPTIONS] SEL_PATH SCORE_PATH STABILITY_PATH OUTPUT_FOLDER

Options

--gene <gene>: Gene (KDT) Symbol to plot its repurposing profile.

--version: Show the version and exit.

Arguments

SEL_PATH: Required argument

SCORE_PATH: Required argument

STABILITY_PATH: Required argument

OUTPUT_FOLDER: Required argument

run

Run the full procedure.

cli run [OPTIONS] DISEASE_PATH

Options

--debug, --no-debug: Flag to run in debug mode.

--verbosity, --no-verbosity: Verbosity level.

--add, --no-add: Check the additivity when computing the SHAP values.

--n-iters <n_iters>: Number of Optimization iterations. 0 means use sensible hyperparameters.

--n-gpus <n_gpus>: Number of CUDA devices, -1 use all decices.

--n-cpus <n_cpus>: Number of CPUs, -1 use all decices.

--version: Show the version and exit.

Arguments

DISEASE_PATH: Required argument

stability

Run the stability analyses.

cli stability [OPTIONS] DISEASE_PATH

Options

--mode <mode>

Options:: train | explain | score

--debug, --no-debug: Flag to run in debug mode.

--verbosity, --no-verbosity: Verbosity level.

--n-iters <n_iters>: Number of Optimization iterations. 0 means use sensible hyperparameters.

--n-gpus <n_gpus>: Number of CUDA devices, -1 use all decices.

--n-cpus <n_cpus>: Number of CPUs, -1 use all decices.

--version: Show the version and exit.

Arguments

DISEASE_PATH: Required argument