Compendium¶

class pyrefinebio.Compendium(id=None, primary_organism_name=None, organism_names=None, svd_algorithm=None, quant_sf_only=None, compendium_version=None, computed_file=None)¶

Retrieve a Compendium based on id

>>> import pyrefinebio
>>> id = 1
>>> result = pyrefinebio.Compendium.get(id)

Retrieve a list of Compendia based on filters

>>> import pyrefinebio
>>> results = pyrefinebio.Compendium.search(primary_organism__name="ACTINIDIA_CHINENSIS")

download(path, prompt=True)¶

Download a Compendium result

Returns:

Compendium

Parameters:

path (str) – the path that the Compendium result should be downloaded to
prompt (bool) – if true, will prompt before downloading files bigger than 1GB

extract()¶

Extract a downloaded Compendium

Returns:: Compendium

classmethod get(id)¶

Retrieve a specific Compendium based on id

Returns:: Compendium
Parameters:: id (int) – the id for the Compendium you want to get

classmethod search(**kwargs)¶

Retrieve a list of Compendium results based on filters

Returns:

list of Compendium

Keyword Arguments:

primary_organism__name (str) – filter based on the name of the primary Organism associated with the compendium
compendium_version (int) – filter based on the Compendium’s version
quant_sf_only (bool) – true for RNA-seq Sample Compendium results or False for quantile normalized
result__id (int) – filter based on the id of the ComputationalResult associated with the compendium
ordering (str) – which field to use when ordering the results
limit (int) – number of results to return per page
offset (int) – the initial index from which to return the results
latest_version (bool) – true will only return the highest compendium_version for each primary_organism