ncbi_genome_download.sh
· 479 B · Bash
Ham
conda create -n ncbi_dl -y -c conda-forge ncbi-datasets-cli jq
for f in batches/batch_*; do
base=$(basename "$f")
out="zips/${base}.zip"
echo "Downloading $f -> $out"
datasets download genome accession --inputfile "$f" \
--include genome,gff3,gbff \
--filename "$out"
# 解压到独立目录（也可以最后统一解压）
mkdir -p "genomes/$base"
unzip -q "$out" -d "genomes/$base"
# 关键：主动降速，避免触发 NCBI 限制
sleep 10
done
| 1 | conda create -n ncbi_dl -y -c conda-forge ncbi-datasets-cli jq |
| 2 | |
| 3 | for f in batches/batch_*; do |
| 4 | base=$(basename "$f") |
| 5 | out="zips/${base}.zip" |
| 6 | |
| 7 | echo "Downloading $f -> $out" |
| 8 | datasets download genome accession --inputfile "$f" \ |
| 9 | --include genome,gff3,gbff \ |
| 10 | --filename "$out" |
| 11 | |
| 12 | # 解压到独立目录（也可以最后统一解压） |
| 13 | mkdir -p "genomes/$base" |
| 14 | unzip -q "$out" -d "genomes/$base" |
| 15 | |
| 16 | # 关键：主动降速，避免触发 NCBI 限制 |
| 17 | sleep 10 |
| 18 | done |