srp-to-gse

srp-to-gse converts a SRA study accession ID (SRP) to GEO accession ID (GSE).

Usage and options

$ pysradb srp-to-gse -h
Usage: pysradb srp-to-gse [OPTIONS] SRP_ID

  Get GSE for a SRP

Options:
  --saveto TEXT  Save output to file
  --detailed     Output additional columns: [sample_accession, run_accession]
  -h, --help     Show this message and exit.

Convert SRA study accession (SRP) to GEO accession ID (GSE)

Gene Expression Omnibus or GEO hosts processed sequencing datasets. The raw data is available through SRA and hence we often need to interpolate between the two.

To convert a SRA study accession of the form SRPmmmmm to its corresponding GEO experiment with ID of the form GSEnnnn:

$ pysradb srp-to-gse SRP098789

study_accession study_alias
SRP098789       GSE94454

In order to obtain detailed metadata:

$ pysradb srp-to-gse --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-gse --detailed --saveto SRP098789_metadata.tsv SRP098789