srp-to-srr

srp-to-srr converts a SRA study accession (SRP) to corresponding SRA run accession(s) (SRR).

Usage and options

$ pysradb srp-to-srr -h

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

  Get SRR for a SRP

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

Convert SRA study accession (SRP) to SRA run accession(s) (SRR)

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

$ pysradb srp-to-srr SRP098789

study_accession run_accession
SRP098789       SRR5227288
SRP098789       SRR5227289
SRP098789       SRR5227290
SRP098789       SRR5227291
SRP098789       SRR5227292
SRP098789       SRR5227293
SRP098789       SRR5227294
SRP098789       SRR5227295
SRP098789       SRR5227296
SRP098789       SRR5227297
SRP098789       SRR5227298
SRP098789       SRR5227299
SRP098789       SRR5227300
SRP098789       SRR5227301
SRP098789       SRR5227302
SRP098789       SRR5227303
SRP098789       SRR5227304
SRP098789       SRR5227305
SRP098789       SRR5227306
SRP098789       SRR5227307
SRP098789       SRR5227308
SRP098789       SRR5227309
SRP098789       SRR5227310
SRP098789       SRR5227311
SRP098789       SRR5227312
SRP098789       SRR5227313

In order to obtain detailed metadata:

$ pysradb srp-to-srr --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-srr --detailed SRP098789_metadata.tsv SRP098789