srr-to-srs

srr-to-srs converts a SRA run accession (SRR) to corresponding SRA sample accession (SRS).

Usage and options

$ pysradb srr-to-srs -h

Usage: pysradb srr-to-srs [OPTIONS] SRR_IDS...

  Get SRS for a SRR

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

Convert SRA run accession (SRR) to SRA sample accession (SRS)

To convert a SRA run accession of the form SRRmmmmm to its corresponding SRA sample accession of the form SRSnnnn:

$ pysradb srr-to-srs SRR1608490

run_accession sample_accession
SRR1608490    SRS718878

In order to obtain detailed metadata:

$ pysradb srr-to-srs --detailed SRR1608490

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 srr-to-srs --detailed --saveto SRR1608490_metadata.tsv SRR1608490