#!/bin/bash
# Reference: NCBI Datasets CLI 16.0+ | Verify API if version differs
# Single-assembly download with auto MD5 + multiple file types.

set -euo pipefail

ACC="${1:-GCF_000001405.40}"   # default: human GRCh38 RefSeq reference
OUT_ZIP="${2:-genome.zip}"
INCLUDE="${3:-genome,gff3,gtf,protein,cds,seq-report}"

echo "=== Download ${ACC} (${INCLUDE}) ==="
datasets download genome accession "${ACC}" \
    --include "${INCLUDE}" \
    --filename "${OUT_ZIP}" \
    --no-progressbar

echo
echo "=== Unzip ==="
DEST="${OUT_ZIP%.zip}"
unzip -q "${OUT_ZIP}" -d "${DEST}/"
ls -lh "${DEST}/ncbi_dataset/data/${ACC}/"

echo
echo "=== Inspect with dataformat (extract metadata from data report JSON) ==="
JSONL="${DEST}/ncbi_dataset/data/assembly_data_report.jsonl"
if [ -f "${JSONL}" ]; then
    dataformat tsv genome \
        --inputfile "${JSONL}" \
        --fields accession,organism-name,assembly-level,scaffold-n50,contig-n50,total-sequence-length \
        | column -t
fi

echo
echo "Datasets auto-verifies MD5 -- no manual checksum step needed."