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