#! /bin/bash
set -e
TMP=${TMP:-"$PROJECTHOME/tmp"}

if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <transcripts_fasta> <swissprot_database> <output_directory>"
    echo "Predict coding sequences (CDS) from transcripts using TD2 and MMseqs2"
    exit 1
fi
transcripts=$1
sprot=$2
outdir=$3

mkdir -p "$outdir"
TD2.LongOrfs -t "$transcripts" --precise -@ 8 -O "$outdir"
mmseqs easy-search "$outdir/longest_orfs.pep" "$sprot" "$outdir/mmseqs.m8" "$TMP" -s 7.0 --threads 16
TD2.Predict -t "$transcripts" --precise -O "$outdir" --retain-mmseqs-hits "$outdir/mmseqs.m8"
echo "CDS prediction completed. Results are in $outdir"