Kingfisher下载SRA数据
文章目录
我知道一个SRP的编号,里面有我想要下载的数据,我想根据SRP编号快速下载数据,查到了Kingfisher这个工具。
https://github.com/wwood/kingfisher-download
文档:https://wwood.github.io/kingfisher-download/
安装:pip install kingfisher
主要有三个模块,get、extract、annotate
get
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extract
将SRA格式转成fastq或者fasta格式
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annotate
根据Run注释,比如碱基数目,BioSample属性等,得到metatable。
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示例
Download .fastq.gz files of the run ERR1739691 from the ENA, or failing that, download an .sra file from the Amazon AWA Open Data Program and then convert to FASTQ (not FASTQ.GZ), or failing that use NCBI prefetch to download and convert that to FASTQ. Output files are put into the current working directory.
$ kingfisher get -r ERR1739691 -m ena-ascp aws-http prefetch
Download a .sra from GCP using a service account key with “gcp cp”. Payment is required.
$ kingfisher get -r ERR1739691 -m gcp-cp -f sra –gcp-user-key-file sa-private-key.json –allow-paid
Download a .sra from the free AWS open data program using 8 threads for download and extraction, coverting to FASTA.
$ kingfisher get -r ERR1739691 -m aws-http -f fasta –download-threads 8
Myself
kingfisher get –bioprojects SRP**** –download-methods ena-ascp –ascp-ssh-key ~/miniconda3/envs/download/etc/asperaweb_id_dsa.openssh
文章作者 zzx
上次更新 2023-11-23