download

download

Fetch public data from an accession.

fa.download("GSE182991") and the files appear, cached, checksummed and with a normalised sample table beside them. The point is not to save typing – it is that the alternative, everybody writing their own GEO scraper, is why two analyses of the same accession routinely start from different files.

Sources are dispatched on the shape of the accession. Credentialed archives (dbGaP, EGA, Synapse, UK Biobank) are documented and deliberately not automated: the access agreement is between the user and the archive, and a tool that made it one function call would be inviting people to breach it.

Functions

Name	Description
clear_cache	Delete the download cache. Returns the bytes freed.
download	Fetch by accession, dispatching on its shape.
how_to_get	The next step for one intervention study, printed for a human.

clear_cache

download.clear_cache(cache_dir=None, *, confirm=False)

Delete the download cache. Returns the bytes freed.

download

download.download(accession, *, cache_dir=None, dry_run=False, **kw)

Fetch by accession, dispatching on its shape.

fa.download(“GSE182991”) fa.download(“GSE182991”, want=“suppl”, dry_run=True)

how_to_get

download.how_to_get(study_id)

The next step for one intervention study, printed for a human.

print(fa.download.how_to_get(“calerie”))