def get_information(protein_id, session=None):
"""
information = get_information(protein_id, session={backend.create_session()})
Returns all information on the protein identified by `protein_id`
Parameters
----------
protein_id : string
protein ID in one of the formats accepted by Waldo
session : database connection, optional
database connection to use
Returns
-------
information : string
CSV representation of all information on `protein_id`
"""
def get_data(module):
spec_id = module.from_ensembl_gene_id(ensemblgene, session)
if not spec_id:
return "None, None"
locs = module.retrieve_go_annotations(spec_id)
all_locs = []
for ls in locs:
all_locs.extend([loc.strip() for loc in re.split("[,.;:]+", ls)])
all_locs = list(set(all_locs))
all_locs = ";".join(all_locs)
url = module.gen_url(spec_id)
return "%s,%s" % (all_locs, url)
if session is None:
session = waldo.backend.create_session()
ensemblgene = translate(protein_id, get_id_namespace(protein_id), "ensembl:gene_id", session)
return ",".join(
[
ensemblgene,
get_data(waldo.uniprot.retrieve),
get_data(waldo.mgi.retrieve),
get_data(waldo.locate.retrieve),
get_data(waldo.hpa.retrieve),
]
)
def test_get_id_namespace():
assert get_id_namespace('ENSGALG00000001190') == 'ensembl:gene_id'
assert get_id_namespace('ENSGALP00000001190') == 'ensembl:peptide_id'
assert get_id_namespace('MGI:1918918') == 'mgi:id'
assert get_id_namespace('2AAA_MOUSE') == 'uniprot:name'
