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# !/usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Generates lists of trees and dendropy.TreeList for tests.
"""
import dendropy
DEFAULT_NUM_TREES = 5
_TREE_COUNTER = 0
def get_tree(taxon_namespace=None,
label=None,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False):
global _TREE_COUNTER
_TREE_COUNTER += 1
if taxon_namespace is None:
taxon_namespace = dendropy.TaxonNamespace()
if label is None:
label = "Tree{}".format(_TREE_COUNTER)
t1 = dendropy.Tree(label=label,
taxon_namespace=taxon_namespace)
t1.seed_node.label = "i0"
c1 = t1.seed_node.new_child(label="i1")
c2 = t1.seed_node.new_child(label="i2")
c1.new_child(label="t1")
c1.new_child(label="t2")
c2.new_child(label="t3")
c2.new_child(label="t4")
tax_labels = set()
for nd in t1:
is_leaf = nd.is_leaf()
if is_leaf and not suppress_leaf_node_taxa:
tax1 = t1.taxon_namespace.require_taxon(nd.label)
nd.taxon = tax1
tax_labels.add(nd.label)
elif (not is_leaf) and not suppress_internal_node_taxa:
tax1 = t1.taxon_namespace.require_taxon(nd.label)
nd.taxon = tax1
tax_labels.add(nd.label)
t1.tax_labels = tax_labels
try:
t1.taxon_namespace.tax_labels.update(tax_labels)
except AttributeError:
t1.taxon_namespace.tax_labels = set(tax_labels)
return t1
def get_trees(
num_trees,
taxon_namespace=None,
label=None,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False):
trees = []
for idx in range(num_trees):
t1 = get_tree(
taxon_namespace=taxon_namespace,
label=label,
suppress_internal_node_taxa=suppress_internal_node_taxa,
suppress_leaf_node_taxa=suppress_leaf_node_taxa)
trees.append(t1)
return trees
def get_tree_list(
num_trees,
taxon_namespace=None,
label=None,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False):
if taxon_namespace is None:
taxon_namespace = dendropy.TaxonNamespace()
tlist1 = dendropy.TreeList(label="1",
taxon_namespace=taxon_namespace)
for idx in range(num_trees):
t1 = get_tree(
taxon_namespace=taxon_namespace,
label=label,
suppress_internal_node_taxa=suppress_internal_node_taxa,
suppress_leaf_node_taxa=suppress_leaf_node_taxa)
assert t1.taxon_namespace is tlist1.taxon_namespace
tlist1.append(t1)
return tlist1
def get_tree_list_and_list_of_trees(
num_trees,
tree_list_taxon_namespace=None,
list_of_trees_taxon_namespace=None):
tlist = get_tree_list(
num_trees=0,
taxon_namespace=tree_list_taxon_namespace,
label=None,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
trees = get_trees(
num_trees=num_trees,
taxon_namespace=list_of_trees_taxon_namespace,
label=None,
suppress_internal_node_taxa=False,
suppress_leaf_node_taxa=False)
return tlist, trees
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