tanghaibao / goatools

from goatools.test_data.checks import _chk_a2bset

def test_get_parent(prt=sys.stdout):

    """Semantic Similarity test for Issue #86."""

    # Load GO-DAG

    fin_obo = "go-basic.obo"

    repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")

    godag = get_godag(os.path.join(repo, fin_obo))

    go2obj = {go:o for go, o in godag.items() if go == o.id}

    # Get all parents for all GO IDs using get_all_parents in GOTerm class

    tic = timeit.default_timer()

    go2parents_orig = {}

    for goobj in go2obj.values():

        go2parents_orig[goobj.id] = goobj.get_all_parents()

    tic = prt_hms(tic, "Get all goobj's parents using GOTerm.get_all_parents()", prt)

    # Get all parents for all GO IDs using GOTerm get_all_parents

    go2parents_fast = get_go2parents(go2obj.values())

    prt_hms(tic, "Get all goobj's parents using go_tasks::get_go2parents", prt)

    # Compare parent lists

    _chk_a2bset(go2parents_orig, go2parents_fast)

    print("PASSED: get_parent test")

if __name__ == '__main__':

from goatools.test_data.checks import _chk_a2bset

def test_get_children(prt=sys.stdout):

    """Semantic Similarity test for Issue #86."""

    # Load GO-DAG

    fin_obo = "go-basic.obo"

    repo = os.path.join(os.path.dirname(os.path.abspath(__file__)), "..")

    godag = get_godag(os.path.join(repo, fin_obo))

    go2obj = {go:o for go, o in godag.items() if go == o.id}

    # Get all children for all GO IDs using get_all_children in GOTerm class

    tic = timeit.default_timer()

    go2children_orig = {}

    for goobj in go2obj.values():

        go2children_orig[goobj.id] = goobj.get_all_children()

    tic = prt_hms(tic, "Get all goobj's children using GOTerm.get_all_children()", prt)

    # Get all children for all GO IDs using GOTerm get_all_children

    go2children_fast = get_go2children(go2obj.values())

    prt_hms(tic, "Get all goobj's children using go_tasks::get_go3children", prt)

    # Compare children lists

    _chk_a2bset(go2children_orig, go2children_fast)

if __name__ == '__main__':