class Test_nodedistributionsetup(unittest.TestCase):
"""
Test class for creating graphical model scaffolds from phylogeny files
"""
def setUp(self):
"""
Loads a phylogeny.
"""
phylo_file = os.path.dirname(os.path.realpath(__file__)) + "/example_data/Asp_protease_2.xml"
self.phylo_graph = BioBayesGraph()
self.graph = self.phylo_graph.populate_from_phyloxml(phylo_file)
def testSetLeafNodeVariableInitialization(self):
"""
Tries to set up graphical model leaf node variables properly.
"""
# Sets all nodes to have 3 variables each.
# And defines the domain of each explicitly
card_sum1 = 0.0
for node_index in self.phylo_graph.iterleafnodes():
# print graph.vertex_properties["name"][graph.vertex(node_index)]
self.phylo_graph.set_node_variable_count(node_index=node_index, num_vars=3)
# So var1 can take values in 0 or 1,
# var2 can take values in {0,1,2,3}
# and var3 can take values in {'a','b','c'}
self.phylo_graph.set_node_variable_domains(
node_index=node_index, var_domains=[(0, 1), (0, 1, 2, 3), ("a", "b", "c")]
)
for v_ind in range(self.phylo_graph.get_node_variable_count(node_index)):
card_sum1 += len(self.phylo_graph.get_node_variable_domain(node_index, v_ind))
self.assertEqual(card_sum1, 2745.0, "Leaf node variable cardinality sum check didn't pass") # 305*(2+4+3)
def testSetInternalNodeVariableInitialization(self):
"""
Tries to set up graphical model internal node variables properly.
"""
card_sum2 = 0.0
for node_index in self.phylo_graph.iterinternalnodes():
# print graph.vertex_properties["name"][graph.vertex(node_index)]
self.phylo_graph.set_node_variable_count(node_index=node_index, num_vars=3)
# So var1 can take values in 0 or 1,
# var2 can take values in {0,1,2,3}
# and var3 can take values in {'a','b','c'}
self.phylo_graph.set_node_variable_domains(node_index=node_index, var_domains=[(0, 1), (0, 1), (0, 1)])
for v_ind in range(self.phylo_graph.get_node_variable_count(node_index)):
card_sum2 += len(self.phylo_graph.get_node_variable_domain(node_index, v_ind))
self.assertEqual(card_sum2, 1818.0, "Internal node variable cardinality sum check didn't pass") # 303*(2+2+2)
def testProbabilityDistInitialization(self):
"""
Tries to set probability distributions for leaf nodes.
"""
self.testSetLeafNodeVariableInitialization()
card_sum1 = 0.0
for node_index in self.phylo_graph.iterleafnodes():
# print graph.vertex_properties["name"][graph.vertex(node_index)]
self.phylo_graph.set_node_variable_count(node_index=node_index, num_vars=3)
for v_ind in range(self.phylo_graph.get_node_variable_count(node_index)):
card_sum1 += len(self.phylo_graph.get_node_variable_domain(node_index, v_ind))
self.assertEqual(card_sum1, 2745.0, "Leaf node variable cardinality sum check didn't pass") # 305*(2+4+3)
