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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.
##
##############################################################################
"""
Tests of birth-death model fitting.
"""
import unittest
import dendropy
from dendropy.test.support.mockrandom import MockRandom
from dendropy.test.support import pathmap
from dendropy.model import coalescent
from dendropy.simulate import popgensim
class TruncatedCoalescentTreeTest(unittest.TestCase):
def get_species_tree(self, ntax=10):
_RNG = MockRandom()
ages = [_RNG.randint(1000,10000) for age in range(ntax)]
ages.sort()
pop_sizes = [_RNG.randint(1000,10000) for pop in range(2*ntax+1)]
taxon_namespace = dendropy.TaxonNamespace(["t{}".format(i+1) for i in range(ntax)])
species_tree = popgensim.pop_gen_tree(taxon_namespace=taxon_namespace,
ages=ages,
num_genes=4,
pop_sizes=pop_sizes,
rng=_RNG)
ages2 = []
for node in species_tree.postorder_node_iter():
distance_from_tip = node.distance_from_tip()
if distance_from_tip > 0:
ages2.append(distance_from_tip)
ages2.sort()
for index in range(len(ages2)):
assert (ages[index] - ages2[index]) < 10e-6
pop_sizes2 = []
for edge in species_tree.postorder_edge_iter():
pop_sizes2.append(edge.pop_size)
pop_sizes2.sort()
return species_tree
def runTest(self, ntax=10):
"""TruncatedCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
species_tree = self.get_species_tree(ntax)
gene_trees = []
while len(gene_trees) < 20:
gene_trees.append(coalescent.constrained_kingman_tree(species_tree)[0])
class PureCoalescentTreeTest(unittest.TestCase):
def runTest(self):
"""PureCoalescentTreeTest -- tree generation without checking [TODO: checks]"""
_RNG = MockRandom()
tns = dendropy.TaxonNamespace(["t{}".format(i+1) for i in range(100)])
t = coalescent.pure_kingman_tree(tns, rng=_RNG)
assert t._debug_tree_is_valid()
if __name__ == "__main__":
unittest.main()
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