def extract_coalescent_frames(*args, **kwargs):
deprecate.dendropy_deprecation_warning(
preamble="Deprecated since DendroPy 4: The 'dendropy.coalescent' module has moved to 'dendropy.model.coalescent'.",
old_construct="from dendropy import coalescent\ncoalescent.extract_coalescent_frames(...)",
new_construct="from dendropy.model import coalescent\ncoalescent.extract_coalescent_frames(...)")
return coalescent.extract_coalescent_frames(*args, **kwargs)
def compile(
self,
tree,
tree_phylogenetic_distance_matrix=None,
tree_node_distance_matrix=None,
):
if self.is_measure_edge_lengths:
if self.is_normalize:
tree_length_nf = tree.length()
if tree_length_nf == 0:
tree_length_nf = 1.0
else:
tree_length_nf = 1.0
self.measurement_profiles["Edge.Lengths"] = MeasurementProfile(
profile_data=[
float(e.length) / tree_length_nf
for e in tree.postorder_edge_iter() if e.length is not None
])
if self.is_measure_patristic_distances or self.is_measure_patristic_steps:
if tree_phylogenetic_distance_matrix is None:
tree_phylogenetic_distance_matrix = tree.phylogenetic_distance_matrix(
)
if self.is_measure_patristic_distances:
self.measurement_profiles[
"Patristic.Distances"] = MeasurementProfile(
profile_data=tree_phylogenetic_distance_matrix.
distances(
is_weighted_edge_distances=True,
is_normalize_by_tree_size=self.is_normalize,
))
if self.is_measure_patristic_steps:
self.measurement_profiles[
"Patristic.Steps"] = MeasurementProfile(
profile_data=tree_phylogenetic_distance_matrix.
distances(
is_weighted_edge_distances=False,
is_normalize_by_tree_size=self.is_normalize,
))
if self.is_measure_node_distances or self.is_measure_node_steps:
if tree_node_distance_matrix is None:
tree_node_distance_matrix = tree.node_distance_matrix()
if self.is_measure_node_distances:
self.measurement_profiles[
"Node.Distances"] = MeasurementProfile(
profile_data=tree_node_distance_matrix.distances(
is_weighted_edge_distances=True,
is_normalize_by_tree_size=self.is_normalize,
))
if self.is_measure_node_steps:
self.measurement_profiles["Node.Steps"] = MeasurementProfile(
profile_data=tree_node_distance_matrix.distances(
is_weighted_edge_distances=False,
is_normalize_by_tree_size=self.is_normalize,
))
if self.is_measure_node_ages:
node_ages = tree.calc_node_ages(
ultrametricity_precision=self.ultrametricity_precision)
if self.is_normalize:
s = sum(node_ages)
try:
normalized_node_ages = [a / s for a in node_ages]
node_ages = normalized_node_ages
except ZeroDivisionError as e:
if self.is_skip_normalization_on_zero_division_error:
pass
else:
raise
self.measurement_profiles["Node.Ages"] = MeasurementProfile(
profile_data=node_ages, )
if self.is_measure_coalescence_intervals:
cf = coalescent.extract_coalescent_frames(
tree=tree,
ultrametricity_precision=self.ultrametricity_precision,
)
waiting_times = cf.values()
if self.is_normalize:
s = sum(waiting_times)
try:
normalized_waiting_times = [w / s for w in waiting_times]
waiting_times = normalized_waiting_times
except ZeroDivisionError as e:
if self.is_skip_normalization_on_zero_division_error:
pass
else:
raise
self.measurement_profiles[
"Coalescence.Intervals"] = MeasurementProfile(
profile_data=waiting_times, )
def compile(self, tree,
tree_phylogenetic_distance_matrix=None,
tree_node_distance_matrix=None,
):
if self.is_measure_edge_lengths:
if self.is_normalize:
tree_length_nf = tree.length()
if tree_length_nf == 0:
tree_length_nf = 1.0
else:
tree_length_nf = 1.0
self.measurement_profiles["Edge.Lengths"] = MeasurementProfile(
profile_data=[float(e.length)/tree_length_nf for e in tree.postorder_edge_iter() if e.length is not None])
if self.is_measure_patristic_distances or self.is_measure_patristic_steps:
if tree_phylogenetic_distance_matrix is None:
tree_phylogenetic_distance_matrix = tree.phylogenetic_distance_matrix()
if self.is_measure_patristic_distances:
self.measurement_profiles["Patristic.Distances"] = MeasurementProfile(
profile_data=tree_phylogenetic_distance_matrix.distances(
is_weighted_edge_distances=True,
is_normalize_by_tree_size=self.is_normalize,))
if self.is_measure_patristic_steps:
self.measurement_profiles["Patristic.Steps"] = MeasurementProfile(
profile_data=tree_phylogenetic_distance_matrix.distances(
is_weighted_edge_distances=False,
is_normalize_by_tree_size=self.is_normalize,))
if self.is_measure_node_distances or self.is_measure_node_steps:
if tree_node_distance_matrix is None:
tree_node_distance_matrix = tree.node_distance_matrix()
if self.is_measure_node_distances:
self.measurement_profiles["Node.Distances"] = MeasurementProfile(
profile_data=tree_node_distance_matrix.distances(
is_weighted_edge_distances=True,
is_normalize_by_tree_size=self.is_normalize,))
if self.is_measure_node_steps:
self.measurement_profiles["Node.Steps"] = MeasurementProfile(
profile_data=tree_node_distance_matrix.distances(
is_weighted_edge_distances=False,
is_normalize_by_tree_size=self.is_normalize,))
if self.is_measure_node_ages:
node_ages = tree.calc_node_ages(ultrametricity_precision=self.ultrametricity_precision)
if self.is_normalize:
s = sum(node_ages)
try:
normalized_node_ages = [a/s for a in node_ages]
node_ages = normalized_node_ages
except ZeroDivisionError as e:
if self.is_skip_normalization_on_zero_division_error:
pass
else:
raise
self.measurement_profiles["Node.Ages"] = MeasurementProfile(profile_data=node_ages,)
if self.is_measure_coalescence_intervals:
cf = coalescent.extract_coalescent_frames(
tree=tree,
ultrametricity_precision=self.ultrametricity_precision,)
waiting_times = cf.values()
if self.is_normalize:
s = sum(waiting_times)
try:
normalized_waiting_times = [w/s for w in waiting_times]
waiting_times = normalized_waiting_times
except ZeroDivisionError as e:
if self.is_skip_normalization_on_zero_division_error:
pass
else:
raise
self.measurement_profiles["Coalescence.Intervals"] = MeasurementProfile(profile_data=waiting_times,)