gse-to-gsm

gse-to-gsm provides list of GEO experiments (GSM) for a GEO study accession (GSE).

Usage and options

$ pysradb gse-to-gsm

Usage: pysradb gse-to-gsm [OPTIONS] GSE_IDS...

  Get SRP for a GSE

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

Convert GEO accession ID (GSE) to GEO expriment accession (GSM)

Getting GSMs from GSE is straight forward:

$ pysradb gse-to-gsm GSE41637 | head

study_alias experiment_alias
GSE41637    GSM1020640_1
GSE41637    GSM1020641_1
GSE41637    GSM1020642_1
GSE41637    GSM1020643_1
GSE41637    GSM1020644_1
GSE41637    GSM1020645_1
GSE41637    GSM1020646_1
GSE41637    GSM1020647_1
GSE41637    GSM1020648_1

To get detailed output:

$ pysradb gse-to-gsm --detailed GSE41637

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 gse-to-gsm --detailed --saveto GSE41637_metadata.tsv GSE41637