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4516781 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | #!/usr/bin/env bash
set -euo pipefail
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
PROJECT_DIR="$(cd "${SCRIPT_DIR}/.." && pwd)"
if [[ -n "${ONESCIENCE_DATASETS_DIR:-}" ]]; then
DATA_ROOT_DIR="${ONESCIENCE_DATASETS_DIR}/AlphaGenome"
else
DATA_ROOT_DIR="${PROJECT_DIR}/data"
fi
if [[ -n "${ONESCIENCE_MODELS_DIR:-}" ]]; then
MODEL_ROOT_DIR="${ONESCIENCE_MODELS_DIR}/AlphaGenome"
else
MODEL_ROOT_DIR="${PROJECT_DIR}/weight"
fi
export PYTHONPATH="${PROJECT_DIR}:${PYTHONPATH:-}"
python "${SCRIPT_DIR}/run_inference.py" \
--fasta_path "${DATA_ROOT_DIR}/reference/HOMO_SAPIENS/GRCh38.p13.genome.fa" \
--model_dir "${MODEL_ROOT_DIR}/alphagenome-all-folds" \
--chromosome chr19 \
--start 10587331 \
--end 11635907 \
--output_dir "${PROJECT_DIR}/outputs"
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