#! /bin/bash
set -e
SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
THREADS=${THREADS:-12}

if [ "$#" -ne 5 ]; then
    echo "Usage: $0 <ogs_dir> <hmmsearch_result_dir> <all_cds.fa> <output_dir> <homolog_stem>"
    echo "Integrate hmmsearch results to new orthologous groups directory and perform MACSE alignment"
    exit 1
fi

ogs_dir=$(readlink -f "$1")
search_dir=$(readlink -f "$2")
all_cds=$(readlink -f "$3")
out_dir=$4
stem=$5

echo "Integrating hmmsearch results to new orthologous groups directory..."
python3 "$SCRIPTS"/miscs/hmmsearch_result_to_new_ogs_dir.py \
    -d "$ogs_dir" \
    -t "$search_dir" \
    -f "$all_cds" \
    -o "$out_dir" \
    -s "$stem"
echo "Integration completed."

echo "Starting MACSE alignment of orthologous groups..."
echo -n >macse.cmds
for og_dir in "$out_dir"/ogs/*; do
    j=$(basename "$og_dir")
    echo "cd $og_dir && bash $SCRIPTS/miscs/macse.sh ${j}_${stem}.fa ${j}.fa $j" >>macse.cmds
done
xargs -t -P "$THREADS" -I cmd -a macse.cmds bash -c "cmd"
echo "MACSE alignment completed."