srr-to-srx

srr-to-srx converts a SRA run accession (SRR) to corresponding SRA sample accession (SRX).

Usage and options

$ pysradb srr-to-srx -h

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

  Get SRX for a SRR

Options:
  --detailed     Output additional columns: [sample_accession (SRS),
                 study_accession (SRP),
                 run_alias (GSM_r),
                 experiment_alias
                 (GSM),
                 sample_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 experiment accession of the form SRXnnnn:

$ pysradb srr-to-srx SRR1608490

run_accession experiment_accession
SRR1608490    SRX729552

In order to obtain detailed metadata:

$ pysradb srr-to-srx --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-srx --detailed --saveto SRR1608490_metadata.tsv SRR1608490