conda activate bpnet

EXPERIMENT_DIRS=("$@")
for EXPERIMENT_DIR in "${EXPERIMENT_DIRS[@]}"; do
    echo $EXPERIMENT_DIR
    mkdir $EXPERIMENT_DIR
    cd $EXPERIMENT_DIR

    # Copy over experiment bigwig files
    cp /oak/stanford/groups/kasowski/data/Cell_Lines_Ped_Leukemia/RUNX1_RUNX1T1/data/$EXPERIMENT_DIR/*.bw .
    cp /oak/stanford/groups/kasowski/data/Cell_Lines_Ped_Leukemia/RUNX1_RUNX1T1/data/$EXPERIMENT_DIR/*.bw .

    # Copy over prediction bigwig files
    cp /oak/stanford/groups/akundaje/shouvikm/BPNet/predictions/$EXPERIMENT_DIR/predictions_plus_avg.bw .
    cp /oak/stanford/groups/akundaje/shouvikm/BPNet/predictions/$EXPERIMENT_DIR/predictions_minus_avg.bw .

    # Copy over contribution bigwig files
    cp /oak/stanford/groups/akundaje/shouvikm/BPNet/contributions/$EXPERIMENT_DIR/counts_scores_avg.bw .
    cp /oak/stanford/groups/akundaje/shouvikm/BPNet/contributions/$EXPERIMENT_DIR/profile_scores_avg.bw .

    # Copy over and sort+index peak file
    cp /oak/stanford/groups/kasowski/data/Cell_Lines_Ped_Leukemia/RUNX1_RUNX1T1/data/$EXPERIMENT_DIR/idr_peaks/peaks_inliers.bed .
    sort -k1,1 -k2,2n peaks_inliers.bed > peaks_inliers.sorted.bed
    bgzip peaks_inliers.sorted.bed
    tabix -p bed peaks_inliers.sorted.bed.gz

    # # Copy over finemo hits file
    # cp /users/shouvikm/BPNet/finemo/$EXPERIMENT_DIR/hits.bed .
    # sort -k1,1 -k2,2n hits.bed > hits.sorted.bed
    # bgzip hits.sorted.bed
    # tabix -p bed hits.sorted.bed.gz

    cd ..
done