def testFittedEdgesDeepCoalCount(self):
for idx, gt in enumerate(self.gene_trees):
ct = reconcile.ContainingTree(containing_tree=self.species_tree,
contained_taxon_set=self.gene_trees.taxon_set,
contained_to_containing_taxon_map=self.gene_taxon_to_population_taxon_map,
contained_trees=[gt],
fit_containing_edge_lengths=True,
)
dc = ct.num_deep_coalescences()
mesqf = pathmap.named_output_stream("ContainingTreeDeepCoalescence_Small_FittedEdges_t%02d_dc%02d.nex" % (idx+1, dc), False)
ct.write_as_mesquite(mesqf)
def testFixedEdgesDeepCoalCount(self):
results = []
for idx, gt in enumerate(self.gene_trees):
ct = reconcile.ContainingTree(containing_tree=self.species_tree,
contained_taxon_set=self.gene_trees.taxon_set,
contained_to_containing_taxon_map=self.gene_taxon_to_population_taxon_map,
contained_trees=[gt],
fit_containing_edge_lengths=False,
)
dc = ct.num_deep_coalescences()
results.append(dc)
mesqf = pathmap.named_output_stream("ContainingTreeDeepCoalescence_Small_FixedEdges_t%02d_dc%02d.nex" % (idx+1, dc), False)
ct.write_as_mesquite(mesqf)
self.assertEqual(results, self.expected_under_original_brlens)
def testFittedEdgesDeepCoalCount(self):
for idx, gt in enumerate(self.gene_trees):
ct = reconcile.ContainingTree(
containing_tree=self.species_tree,
contained_taxon_set=self.gene_trees.taxon_set,
contained_to_containing_taxon_map=self.
gene_taxon_to_population_taxon_map,
contained_trees=[gt],
fit_containing_edge_lengths=True,
)
dc = ct.num_deep_coalescences()
mesqf = pathmap.named_output_stream(
"ContainingTreeDeepCoalescence_Small_FittedEdges_t%02d_dc%02d.nex"
% (idx + 1, dc), False)
ct.write_as_mesquite(mesqf)
def testFixedEdgesDeepCoalCount(self):
results = []
for idx, gt in enumerate(self.gene_trees):
ct = reconcile.ContainingTree(
containing_tree=self.species_tree,
contained_taxon_set=self.gene_trees.taxon_set,
contained_to_containing_taxon_map=self.
gene_taxon_to_population_taxon_map,
contained_trees=[gt],
fit_containing_edge_lengths=False,
)
dc = ct.num_deep_coalescences()
results.append(dc)
mesqf = pathmap.named_output_stream(
"ContainingTreeDeepCoalescence_Small_FixedEdges_t%02d_dc%02d.nex"
% (idx + 1, dc), False)
ct.write_as_mesquite(mesqf)
self.assertEqual(results, self.expected_under_original_brlens)
