1_variant_effect_prediction.sh

#!/usr/bin/env bash

###############################################################
# Example script for running Sei variant effect prediction
# using Selene.

# Usage:
# sh 1_variant_effect_prediction.sh <vcf> <hg> <output-dir> [--cuda]

# Please only specify hg38 or hg19 as input for <hg>.

# --cuda is optional, use if you are running on a CUDA-enabled
# GPU machine (see example_slurm_scripts/1_example_vep.slurm_gpu.sh)
###############################################################

set -o errexit
set -o pipefail
set -o nounset

vcf_filepath="${1:-}"
hg_version="${2:-}"
outdir="${3:-}"
cuda="${4:-}"

mkdir -p $outdir

echo "Input arguments: $vcf_filepath $hg_version $outdir $cuda"

vcf_basename=$(basename $vcf_filepath)
cp $vcf_filepath $outdir/

if [ "$cuda" = "--cuda" ]
then
    echo "use_cuda: True"
    python -u 1_variant_effect_prediction.py \
        "$outdir/$vcf_basename" \
        $outdir \
        --genome=${hg_version} \
        --cuda
else
    echo "use_cuda: False"
    python -u 1_variant_effect_prediction.py \
        "$outdir/$vcf_basename" \
        $outdir \
        --genome=${hg_version}
fi