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

if [ "$#" -ne 2 ]; then
    echo "Usage: $0 <input_fasta> <output_nexus>"
    exit 1
fi

in_fasta=$(readlink -f "$1")
out_nex=$2

# Convert fasta to nexus
out_dir=$(dirname "$out_nex")
mkdir -p "$out_dir"
seqmagick convert --output-format nexus --alphabet dna --input-format fasta "$in_fasta" "$out_nex"
# append MrBayes block to nexus file
cat "$SCRIPTS"/miscs/mbblock.txt >>"$out_nex"
# Run MrBayes
mb "$out_nex" >"${out_dir}"/mrbayes.log 2>&1