ncbi_genome_download.sh
· 1.0 KiB · Bash
Surowy
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
#!/usr/bin/env bash
mkdir -p zips genomes
for f in batches/batch_*; do
base=$(basename "$f")
out="zips/${base}.zip"
dir="genomes/$base"
# 如果已经有对应解压目录，就认为完成，直接跳过
if [[ -d "$dir" ]]; then
echo "SKIP (exists): $dir"
continue
fi
echo "Downloading $f -> $out"
datasets download genome accession --inputfile "$f" \
--include genome,gff3,gbff \
--filename "$out"
mkdir -p "$dir"
unzip -q "$out" -d "$dir"
# 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 |
| 19 | |
| 20 | |
| 21 | #!/usr/bin/env bash |
| 22 | |
| 23 | mkdir -p zips genomes |
| 24 | |
| 25 | for f in batches/batch_*; do |
| 26 | base=$(basename "$f") |
| 27 | out="zips/${base}.zip" |
| 28 | dir="genomes/$base" |
| 29 | |
| 30 | # 如果已经有对应解压目录，就认为完成，直接跳过 |
| 31 | if [[ -d "$dir" ]]; then |
| 32 | echo "SKIP (exists): $dir" |
| 33 | continue |
| 34 | fi |
| 35 | |
| 36 | echo "Downloading $f -> $out" |
| 37 | datasets download genome accession --inputfile "$f" \ |
| 38 | --include genome,gff3,gbff \ |
| 39 | --filename "$out" |
| 40 | |
| 41 | mkdir -p "$dir" |
| 42 | unzip -q "$out" -d "$dir" |
| 43 | |
| 44 | # 主动降速，避免触发 NCBI 限制 |
| 45 | sleep 10 |
| 46 | done |