下载NCBI的SRA数据: pysradb

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

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