这里推荐一个下载NCBI SRA数据的神器,pysradb。这是一个基于python开发的软件,支持从命令行运行,也可以作为python的package直接在python代码中调用。
命令行下所有参数信息:
$ pysradb
usage: pysradb [-h] [--version] [--citation]
{metadata,download,search,gse-to-gsm,gse-to-srp,gsm-to-gse,gsm-to-srp,gsm-to-srr,gsm-to-srs,gsm-to-srx,srp-to-gse,srp-to-srr,srp-to-srs,srp-to-srx,srr-to-gsm,srr-to-srp,srr-to-srs,srr-to-srx,srs-to-gsm,srs-to-srx,srx-to-srp,srx-to-srr,srx-to-srs}
...
pysradb: Query NGS metadata and data from NCBI Sequence Read Archive.
version: 2.0.1
Citation: 10.12688/f1000research.18676.1
optional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
--citation how to cite
subcommands:
{metadata,download,search,gse-to-gsm,gse-to-srp,gsm-to-gse,gsm-to-srp,gsm-to-srr,gsm-to-srs,gsm-to-srx,srp-to-gse,srp-to-srr,srp-to-srs,srp-to-srx,srr-to-gsm,srr-to-srp,srr-to-srs,srr-to-srx,srs-to-gsm,srs-to-srx,srx-to-srp,srx-to-srr,srx-to-srs}
metadata Fetch metadata for SRA project (SRPnnnn)
download Download SRA project (SRPnnnn)
search Search SRA for matching text
gse-to-gsm Get GSM for a GSE
gse-to-srp Get SRP for a GSE
gsm-to-gse Get GSE for a GSM
gsm-to-srp Get SRP for a GSM
gsm-to-srr Get SRR for a GSM
gsm-to-srs Get SRS for a GSM
gsm-to-srx Get SRX for a GSM
srp-to-gse Get GSE for a SRP
srp-to-srr Get SRR for a SRP
srp-to-srs Get SRS for a SRP
srp-to-srx Get SRX for a SRP
srr-to-gsm Get GSM for a SRR
srr-to-srp Get SRP for a SRR
srr-to-srs Get SRS for a SRR
srr-to-srx Get SRX for a SRR
srs-to-gsm Get GSM for a SRS
srs-to-srx Get SRX for a SRS
srx-to-srp Get SRP for a SRX
srx-to-srr Get SRR for a SRX
srx-to-srs Get SRS for a SRX更多教程信息参考: https://saket-choudhary.me/pysradb/quickstart.html

