srp-to-srx

srp-to-srx converts a SRA study accession (SRP) to corresponding SRA experiment accession(s) (SRX).

Usage and options

$ pysradb srp-to-srx -h

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

  Get SRX/SRR for a SRP

Options:
  --saveto TEXT  Save output to file
  --detailed     Output additional columns: [sample_accession (SRS),
                 run_accession (SRR),
                 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 experiment accession (SRX)

To convert a SRA study accession of the form SRPmmmmm to its corresponding SRA experiment accession(s) of the form SRXnnnn:

$ pysradb srp-to-srx SRP098789

experiment_accession study_accession
SRX2536403           SRP098789
SRX2536404           SRP098789
SRX2536405           SRP098789
SRX2536406           SRP098789
SRX2536407           SRP098789
SRX2536408           SRP098789
SRX2536409           SRP098789
SRX2536410           SRP098789
SRX2536411           SRP098789
SRX2536412           SRP098789
SRX2536413           SRP098789
SRX2536414           SRP098789
SRX2536415           SRP098789
SRX2536416           SRP098789
SRX2536417           SRP098789
SRX2536418           SRP098789
SRX2536419           SRP098789
SRX2536420           SRP098789
SRX2536421           SRP098789
SRX2536422           SRP098789
SRX2536423           SRP098789
SRX2536424           SRP098789
SRX2536425           SRP098789
SRX2536426           SRP098789
SRX2536427           SRP098789
SRX2536428           SRP098789

In order to obtain detailed metadata:

$ pysradb srp-to-srx --detailed SRP098789

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-srx --detailed --saveto SRP098789_metadata.tsv SRP098789