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)
