#!/usr/bin/env nix-shell
#! nix-shell -i bash --pure
#! nix-shell -p bash sratoolkit curl unzip

# GENOMES:
# Lc. mesenteroides https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_009913915.1/
# Lb. sakei subsp. sakei 23K https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000026065.1/
# W. koreensis KACC 15510 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000219805.1/
# Lc. gasicomitatum LMG 18811 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000196855.1/
# RAW READS:
# J7, https://www.ncbi.nlm.nih.gov/sra/SRX128699[accn]
# J13, https://www.ncbi.nlm.nih.gov/sra/SRX128700[accn]
# J18, https://www.ncbi.nlm.nih.gov/sra/SRX128702[accn]

fasterq-dump --split-3 SRR443366
fasterq-dump --split-3 SRR443367
fasterq-dump --split-3 SRR443368

gzip *.fastq

curl -o datasets 'https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets'
chmod +x datasets

./datasets download genome accession GCF_009913915.1 --filename GCF_009913915.1.zip
./datasets download genome accession GCF_000026065.1 --filename GCF_000026065.1.zip
./datasets download genome accession GCF_000219805.1 --filename GCF_000219805.1.zip
./datasets download genome accession GCF_000196855.1 --filename GCF_000196855.1.zip

mkdir genomes
for i in *.zip; do unzip -j $i ncbi_dataset/data/*/*.fna -d genomes; done