#! /bin/bash
set -e
THREADS=${THREADS:-12}
EXT=${EXT:-"fa"}

if [ "$#" -ne 2 ]; then
    echo "Usage: $0 <ogs_dir> <out_dir>"
    echo "Perform MACSE alignment for each orthologous group"
    exit 1
fi

ogs_dir=$(readlink -f "$1")
out_dir=$2

mkdir -p "$out_dir"
echo "Starting MACSE alignment of orthologous groups..."
echo -n >macse.cmds
for og_fasta in "$ogs_dir"/*."$EXT"; do
    og_name=$(basename "$og_fasta" ."$EXT")
    out_stem="$out_dir/$og_name"
    echo "macse -prog alignSequences -seq $og_fasta -out_AA ${out_stem}.pal -out_NT ${out_stem}.nal > ${out_stem}.log 2>&1" >>macse.cmds
done
xargs -t -P "$THREADS" -I cmd -a macse.cmds bash -c "cmd" &&
    echo "MACSE alignment completed."