srp-to-srs

srp-to-srs converts a SRA study accession (SRP) to corresponding SRA sample accession(s) (SRS).

Usage and options

Usage: pysradb srp-to-srs [OPTIONS] SRP_ID

  Get SRS for a SRP

Options:
  --saveto TEXT  Save output to file
  --detailed     Output additional columns: [run_accession (SRR),
                 study_accession (SRP),
                 experiment_alias (GSM),
                 sample_alias (GSM_),
                 run_alias (GSM_r),
                 study_alias (GSE)]
  -h, --help     Show this message and exit.

Convert SRA study accession (SRP) to SRA sample accession (SRS)

To convert a SRA study accession of the form SRPmmmmm to its corresponding SRA run accessions of the form SRRnnnn:

$ pysradb srp-to-srs SRP048759 | head

study_accession sample_accession
SRP048759       SRS718878
SRP048759       SRS718879
SRP048759       SRS718880
SRP048759       SRS718881
SRP048759       SRS718882
SRP048759       SRS718883
SRP048759       SRS718884
SRP048759       SRS718885
SRP048759       SRS718886

In order to obtain detailed metadata:

$ pysradb srp-to-srs --detailed SRP048759 | head

Saving metadata to a file

pysradb follows a consistent pattern for providing an option to save output of any of its subcommands to a file using the --saveto argument:

$ pysradb srp-to-srs --detailed --saveto SRP048759_metadata.tsv SRP048759