gse-to-srp

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

Usage and options

$ pysradb gse-to-srp -h

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

  Get SRP for a GSE

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

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

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

$ pysradb gse-to-srp GSE41637

study_alias study_accession
GSE41637    SRP016501

Getting sample attributes

Often, the most useful information is in the expanded metadata. For example, what cell` types do different experiments correspond to? What treatments have been applied to them? This can be obtained by using the -detailed flag:

$ pysradb gse-to-srp --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-srp --detailed --saveto GSE41637_metadata.tsv GSE41637