def test_ilp_simple():
n1 = Node('a', [1, 0, 0, 0, 0])
n2 = Node('b', [1, 0, 0, 1, 0])
n3 = Node('c', [1, 0, 0, 2, 0])
n4 = Node('d', [1, 2, 0, 1, 0])
n5 = Node('e', [1, 1, 0, 1, 0])
n6 = Node('f', [1, 0, 3, 2, 0])
n7 = Node('g', [0, 0, 0, 0, 1])
n8 = Node('h', [0, 1, 0, 0, 1])
n9 = Node('i', [0, 1, 2, 0, 1])
n10 = Node('j', [0, 1, 1, 0, 1])
nodes = [n1, n2, n3, n4, n5, n6, n7, n8, n9, n10]
with open(stdout_backup, "w") as f:
sys.stdout = f
tree = ls.solve_lineage_instance(nodes, method="ilp")
os.remove(stdout_backup)
net = tree.get_network()
roots = [n for n in net if net.in_degree(n) == 0]
assert len(roots) == 1
root = roots[0]
targets = [n for n in net if n.is_target]
assert len(targets) == len(nodes)
for t in targets:
assert nx.has_path(net, root, t)
def test_on_sim_greedy():
stree = pic.load(open("test/data/sim_net.pkl", "rb"))
leaves = stree.get_leaves()
target_nodes = []
for l in leaves:
new_node = Node(l.name, l.get_character_vec())
target_nodes.append(new_node)
rtree = ls.solve_lineage_instance(target_nodes, method="greedy")
rnet = rtree.get_network()
roots = [n for n in rnet if rnet.in_degree(n) == 0]
assert len(roots) == 1
root = roots[0]
targets = [n for n in rnet if n.is_target]
assert len(targets) == len(target_nodes)
for t in targets:
assert nx.has_path(rnet, root, t)
multi_parents = [n for n in rnet if rnet.in_degree(n) > 1]
assert len(multi_parents) == 0
def test_ilp_parallel_evo():
n = Node('a', [1, 1, 2, 0])
n2 = Node('b', [1, 1, 3, 0])
n3 = Node('c', [2, 1, 1, 0])
n4 = Node('d', [2, 1, 3, 0])
n5 = Node('e', [1, 3, 1, '-'])
n6 = Node('f', [1, '-', '-', '1'])
n7 = Node('g', [1, 1, 0, 2])
nodes = [n, n2, n3, n4, n5, n6, n7]
with open(stdout_backup, "w") as f:
sys.stdout = f
tree = ls.solve_lineage_instance(nodes, method='ilp')
os.remove(stdout_backup)
net = tree.get_network()
roots = [n for n in net if net.in_degree(n) == 0]
assert len(roots) == 1
root = roots[0]
targets = [n for n in net if n.is_target]
assert len(targets) == len(nodes)
for t in targets:
assert nx.has_path(net, root, t)
multi_parents = [n for n in net if net.in_degree(n) > 1]
assert len(multi_parents) == 0
def test_on_sim_hybrid():
stree = pic.load(open("test/data/sim_net.pkl", "rb"))
leaves = stree.get_leaves()
target_nodes = []
for l in leaves:
new_node = Node(l.name, l.get_character_vec())
target_nodes.append(new_node)
with open(stdout_backup, "w") as f:
sys.stdout = f
rtree = ls.solve_lineage_instance(target_nodes,
method="hybrid",
hybrid_subset_cutoff=200,
time_limit=100,
max_neighborhood_size=500,
threads=4)
os.remove(stdout_backup)
rnet = rtree.get_network()
roots = [n for n in rnet if rnet.in_degree(n) == 0]
assert len(roots) == 1
root = roots[0]
targets = [n for n in rnet if n.is_target]
assert len(targets) == len(target_nodes)
for t in targets:
assert nx.has_path(rnet, root, t)
multi_parents = [n for n in rnet if rnet.in_degree(n) > 1]
assert len(multi_parents) == 0