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

if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <aln_dir> <out_dir> <ext>"
    echo "Build FastTree phylogenetic trees and perform TreeShrink on trimmed MACSE nucleotide alignments"
    exit 1
fi

aln_dir=$(readlink -f "$1")
out_dir=$(readlink -f "$2")
ext=$3

# fasttree
mkdir -p "$out_dir"
echo -n >fasttree.cmds
for i in "$aln_dir"/*."$ext"; do
    j=$(basename "$i" ."$ext")
    mkdir -p "$out_dir"/"${j}"
    cp -s "$i" "$out_dir"/"${j}"/input.fasta
    echo "FastTree -nt -gtr -quiet $out_dir/${j}/input.fasta > $out_dir/${j}/input.tree" >>fasttree.cmds
done
xargs -t -P "$THREADS" -I cmd -a fasttree.cmds bash -c "cmd"
# treeshrink
run_treeshrink.py -f -i "$out_dir"/ -t input.tree -a input.fasta >treeshrink.log