#! /usr/bin/env bash

if [ "$#" -ne 3 ]; then
    echo "Usage: $0 <input_fasta_dir> <extension> <output_nexus_dir>"
    exit 1
fi

input_dir=$1
extension=$2
output_dir=$3
mkdir -p "${output_dir}"
for f in "${input_dir}"/*."${extension}"; do
    filename=$(basename -- "${f}")
    filename_noext="${filename%.*}"
    output_file="${output_dir}/${filename_noext}.nex"
    echo "Converting ${f} to ${output_file}"
    seqmagick convert --output-format nexus --alphabet dna --input-format fasta "${f}" "${output_file}"
done