def test_searcher_get_housekeeping_genes(): """Try to get the list of housekeeping genes. Check a known HK gene.""" searcher = search.Searcher() hk_genes = searcher.get_housekeeping_genes() # check ATF1 in housekeeping genes assert "ENSG00000123268" in hk_genes
def test_searcher_get_transcription_factors(): """Try to get the list of transcription factors. Check a known TF.""" searcher = search.Searcher() tfactors = searcher.get_transcription_factors() # check ATF1 in transcription factors assert "ENSG00000123268" in tfactors
def test_searcher_traverse_vs_namespace(): """Check that traversing the GO with a namespace ID returns the same result as selecting the IDs in the namesapce.""" searcher = search.Searcher() descendants = searcher.traverse(biological_process_id) ids = searcher.select_namespace(biological_process_namespace) assert sorted(descendants) == sorted(ids)
def test_searcher_get_control_genes(): """Try to get the list of control genes. Check a known control gene.""" searcher = search.Searcher() controls = searcher.get_control_genes(0.6) # check AP3S2 in control genes assert "ENSG00000157823" in controls
def test_searcher_traverse(): """Try to traverse the GO for a given GO ID.""" searcher = search.Searcher() descendants = searcher.traverse(biological_process_id)
def test_searcher_get_genes_allbp(): """Try to get all genes associated with IDs in a namespace.""" searcher = search.Searcher() ids = searcher.select_namespace(biological_process_namespace) all_bp_genes = searcher.get_genes(ids)
def test_searcher_get_genes(): """Try to get genes associated with a given GO ID.""" searcher = search.Searcher() bp_genes = searcher.get_genes([biological_process_id])
def test_searcher_select_namespace(): """Try to select all IDs in a given namespace.""" searcher = search.Searcher() ids = searcher.select_namespace(biological_process_namespace)