NCBI 下载fna文件 human viral bacteria

最新推荐文章于 2024-03-17 20:24:56 发布

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最新推荐文章于 2024-03-17 20:24:56 发布 · 1.9k 阅读

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CC 4.0 BY-SA版权

基于manifest 手动批量下载

#!/usr/bin/bash
cat  manifest.txt | while read row
do
path=`dirname $row`
# para -d check dir
if [ ! -d "$path" ]; then
mkdir -p "$path"
fi
# para -f check file
if [ ! -f "$row" ]; then
cd  "$path"
wget -c https://ftp.ncbi.nlm.nih.gov/genomes/${row}
cd -
fi
done

https://ftp.ncbi.nlm.nih.gov/genomes/all
https://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt
manifest.txt模板

all/GCF/001/865/495/GCF_001865495.1_ASM186549v1/GCF_001865495.1_ASM186549v1_genomic.fna.gz
all/GCF/013/372/085/GCF_013372085.1_ASM1337208v1/GCF_013372085.1_ASM1337208v1_genomic.fna.gz
all/GCF/002/079/965/GCF_002079965.1_ASM207996v1/GCF_002079965.1_ASM207996v1_genomic.fna.gz
all/GCF/000/242/855/GCF_000242855.2_ASM24285v2/GCF_000242855.2_ASM24285v2_genomic.fna.gz
all/GCF/902/166/465/GCF_902166465.1_25964_2_27/GCF_902166465.1_25964_2_27_genomic.fna.gz