#! /bin/bash
set -e
SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
IDENTITY=${IDENTITY:-0.99}
THREADS=${THREADS:-6}S

if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <input_dir> <output_dir> <extension>"
    echo "Reduce redundancy of CDS files using cd-hit-est"
    exit 1
fi

indir=$1
outdir=$2
ext=$3

mkdir -p "$outdir"
# Process each file in the input directory with the specified extension
for cds in "$indir"/*."$ext"; do
    stem=$(basename "$cds" ."$ext")
    echo "Processing $cds($stem) ..."
    echo "cd-hit-est -i $cds -o $outdir/$stem.cds_rr.fa -c $IDENTITY -n 10 -r 0 -T $THREADS"
    cd-hit-est -i "$cds" -o "$outdir/$stem".cds_rr.fa -c "$IDENTITY" -n 10 -r 0 -T "$THREADS"
    echo "seqkit translate $outdir/$stem.cds_rr.fa > $outdir/$stem.prot_rr.fa"
    seqkit translate "$outdir/$stem".cds_rr.fa >"$outdir/$stem".prot_rr.fa
    echo "Done."
done