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