def test_three(self):
text = "((4, 5#1)2, (#1, 6)3);"
enewick_graph = enewick_to_digraph(text)
self.assertEqual(len(enewick_graph.nodes()), 6)
enewick_graph = calc_hybrid(enewick_graph)
leafs = get_leaf_nodes(enewick_graph)
gold_leafs = ['1', '4', '6', ]
self.assertItemsEqual(leafs, gold_leafs)
clusters = ["1,2", "2,3"]
gold = construct(clusters)
g = enewick_to_phylonet(text)
GM = GraphMatcher(g, gold)
self.assertTrue(GM.is_isomorphic())
def benchmark_nets(g):
# atributs varis
arestes_llevables = len(removable_edges(g))
fulles = len(get_leaf_nodes(g))
nodes = len(g.nodes())
arestes = len(g.edges())
hibrids = len(hybrid_nodes(g))
grau_hibriditzacio = hybridization_degree(g)
es_treechild = is_treechild(g)
nodes_conflictius = len(problematic_treechild_nodes(g))
subarbres = potential_number_of_calls(g)
temps_soft, temps_soft_cache = -1, -1
n_families, temps_families = -1, -1
# tree-child
# poda amb timeout
# if arestes_llevables > MAX_ARESTES:
# return
if not es_treechild:
try:
log.debug("inici construccio {}".format(arestes_llevables))
executor = ThreadPoolExecutor(max_workers=1)
begin_families = time.time()
future = executor.submit(construct_treechild, g)
families = future.result(TIMEOUT)
end_families = time.time()
temps_families = end_families - begin_families
n_families = len(families)
log.debug("final {}".format(arestes_llevables))
except TimeoutError:
log.debug("timeout {}".format(arestes_llevables))
n_familes, temps_families = -1, -1
else:
n_families, temps_families = 0, 0
BenchmarkCase.create(
test = TEST_NUMBER,
fulles = fulles,
nodes = nodes,
arestes = arestes,
hibrids = hibrids,
subarbres = subarbres,
grau_hibriditzacio = grau_hibriditzacio,
temps_soft = temps_soft,
temps_soft_cache = temps_soft_cache,
arestes_llevables = arestes_llevables,
es_treechild = es_treechild,
nodes_conflictius = nodes_conflictius,
temps_families = temps_families,
n_families = n_families,
)
def test_case(g):
test = TEST_NUMBER
nodes = len(g.nodes())
fulles = len(get_leaf_nodes(g))
arestes = len(g.edges())
hibrids = len(hybrid_nodes(g))
grau_hibriditzacio = hybridization_degree(g)
arestes_llevables = len(removable_edges(g))
es_treechild = is_treechild(g)
nodes_conflictius = len(problematic_treechild_nodes(g))
subarbres = potential_number_of_calls(g)
# soft
if subarbres < MAX_SUBARBRES:
begin_soft = time.time()
cluster_soft_cache(g)
end_soft = time.time()
temps_soft = end_soft - begin_soft
begin_soft_cache = time.time()
for i in range(SOFT_TIMES):
cluster_soft_cache(g)
end_soft_cache = time.time()
temps_soft_cache = (end_soft_cache - begin_soft_cache) / SOFT_TIMES
else:
temps_soft, temps_soft_cache = -1, -1
# tree-child
if not es_treechild:
begin_families = time.time()
families = construct_treechild(g)
end_families = time.time()
n_families = len(families)
temps_families = end_families - begin_families
else:
n_families, temps_families = 0, 0
BenchmarkCase.create(
test = test,
fulles = fulles,
nodes = nodes,
arestes = arestes,
hibrids = hibrids,
subarbres = subarbres,
grau_hibriditzacio = grau_hibriditzacio,
temps_soft = temps_soft,
temps_soft_cache = temps_soft_cache,
arestes_llevables = arestes_llevables,
es_treechild = es_treechild,
nodes_conflictius = nodes_conflictius,
temps_families = temps_families,
n_families = n_families,
)
def enewick_to_digraph(s):
try:
parsed = make_enewick_parser()(s)[0]
except pyparsing.ParseException:
raise MalformedNewickException("Malformed eNewick string")
g = nx.DiGraph()
_walk(g, parsed)
# is_leaf = lambda x: not g.successors(x)
# dfs = lambda x: dfs_preorder_nodes(g, x)
trans_leafs = {}
# remove the initial «#»
for leaf in cluster_networks.get_leaf_nodes(g):
trans_leafs[leaf] = re.sub("#", "", leaf)
g = nx.relabel_nodes(g, trans_leafs)
return g
def benchmark_nets(g):
# atributs varis
arestes_llevables = len(removable_edges(g))
fulles = len(get_leaf_nodes(g))
nodes = len(g.nodes())
arestes = len(g.edges())
hibrids = len(hybrid_nodes(g))
grau_hibriditzacio = hybridization_degree(g)
es_treechild = is_treechild(g)
nodes_conflictius = len(problematic_treechild_nodes(g))
subarbres = potential_number_of_calls(g)
temps_soft, temps_soft_cache = -1, -1
n_families, temps_families = -1, -1
# tree-child
if not es_treechild:
if arestes_llevables < MAX_ARESTES:
begin_families = time.time()
families = construct_treechild(g)
end_families = time.time()
temps_families = end_families - begin_families
n_families = len(families)
else:
n_families, temps_families = 0, 0
BenchmarkCase.create(
test=TEST_NUMBER,
fulles=fulles,
nodes=nodes,
arestes=arestes,
hibrids=hibrids,
subarbres=subarbres,
grau_hibriditzacio=grau_hibriditzacio,
temps_soft=temps_soft,
temps_soft_cache=temps_soft_cache,
arestes_llevables=arestes_llevables,
es_treechild=es_treechild,
nodes_conflictius=nodes_conflictius,
temps_families=temps_families,
n_families=n_families,
)
