def testSummarizeNodeAgesOnMCCT(self):
"""
SumTrees: summarizing node ages on MCCT topology.
"""
if runlevel.is_test_enabled(runlevel.EXHAUSTIVE, _LOG, self.__class__.__name__):
path_to_src = pathmap.tree_source_path("primates.beast.mcmc.trees")
path_to_target = pathmap.tree_source_path("primates.beast.mcct.noedgelens.tree")
args = ["-b",
"40",
"-e",
"mean-age",
"-t",
path_to_target,
path_to_src]
retcode, stdout, stderr = self.execute_sumtrees(args)
self.assertEqual(retcode, 0)
taxa = dendropy.TaxonSet()
exp_tree = dendropy.Tree.get_from_path(pathmap.tree_source_path("primates.beast.mcct.meanh.tre"), "nexus", taxon_set=taxa)
obs_tree = dendropy.Tree.get_from_string(stdout, "nexus", taxon_set=taxa)
exp_tree.update_splits()
exp_tree.calc_node_ages()
obs_tree.update_splits()
obs_tree.calc_node_ages()
self.assertEqual(exp_tree.split_edges.keys(), obs_tree.split_edges.keys())
splits = exp_tree.split_edges.keys()
for split in splits:
exp_edge = exp_tree.split_edges[split]
obs_edge = obs_tree.split_edges[split]
self.assertAlmostEqual(obs_edge.head_node.age, exp_edge.head_node.age)
else:
_LOG.info("Skipping test (set 'DENDROPY_TESTING_LEVEL=EXHAUSTIVE' to run)")
def setUp(self):
self.test_cases = [("pythonidae.reference-trees.nexus", "pythonidae.reference-trees.nexus")]
if runlevel.is_test_enabled(runlevel.SLOW, _LOG, self.__class__.__name__):
self.test_cases.extend(
[
("feb032009.trees.nexus", "feb032009.trees.nexus"),
("maj-rule-bug1.trees.nexus", "maj-rule-bug1.trees.nexus"),
("maj-rule-bug2.trees.nexus", "maj-rule-bug2.trees.nexus"),
]
)
def setUp(self):
self.test_cases = [('pythonidae.reference-trees.nexus',
'pythonidae.reference-trees.nexus')]
if runlevel.is_test_enabled(runlevel.SLOW, _LOG,
self.__class__.__name__):
self.test_cases.extend([
('feb032009.trees.nexus', 'feb032009.trees.nexus'),
('maj-rule-bug1.trees.nexus', 'maj-rule-bug1.trees.nexus'),
('maj-rule-bug2.trees.nexus', 'maj-rule-bug2.trees.nexus'),
])
def testSummarizeNodeAgesOnMCCT(self):
"""
SumTrees: summarizing node ages on MCCT topology.
"""
if runlevel.is_test_enabled(runlevel.EXHAUSTIVE, _LOG,
self.__class__.__name__):
path_to_src = pathmap.tree_source_path("primates.beast.mcmc.trees")
path_to_target = pathmap.tree_source_path(
"primates.beast.mcct.noedgelens.tree")
args = [
"-b", "40", "-e", "mean-age", "-t", path_to_target, path_to_src
]
retcode, stdout, stderr = self.execute_sumtrees(args)
self.assertEqual(retcode, 0)
taxa = dendropy.TaxonSet()
exp_tree = dendropy.Tree.get_from_path(
pathmap.tree_source_path("primates.beast.mcct.meanh.tre"),
"nexus",
taxon_set=taxa)
obs_tree = dendropy.Tree.get_from_string(stdout,
"nexus",
taxon_set=taxa)
exp_tree.update_splits()
exp_tree.calc_node_ages()
obs_tree.update_splits()
obs_tree.calc_node_ages()
self.assertEqual(exp_tree.split_edges.keys(),
obs_tree.split_edges.keys())
splits = exp_tree.split_edges.keys()
for split in splits:
exp_edge = exp_tree.split_edges[split]
obs_edge = obs_tree.split_edges[split]
self.assertAlmostEqual(obs_edge.head_node.age,
exp_edge.head_node.age)
else:
_LOG.info(
"Skipping test (set 'DENDROPY_TESTING_LEVEL=EXHAUSTIVE' to run)"
)
def testSimple(self):
if not is_test_enabled(runlevel.SLOW, _LOG, module_name=__name__, message="skipping all rotation scm tests"):
return
clades = ['A', 'D', None, None]
for m in [0, 1]:
four_sisters = ['B', 'C']
clades[2] = '(%s,%s)' % (four_sisters[m], four_sisters[1-m])
for i in [0, 1, 2]:
for j in [0, 1, 2]:
if i == j:
continue
k = [0, 1, 2]
k.remove(i)
k.remove(j)
k = k[0]
base = [clades[i], clades[j], clades[k]]
four_taxon_newick = '(%s);' % ','.join(base)
for ii in [0, 1, 2]:
for jj in [0, 1, 2]:
if ii == jj:
continue
kk = [0, 1, 2]
kk.remove(ii)
kk.remove(jj)
kk = kk[0]
base = [clades[ii], clades[jj], clades[kk]]
for n in range(4):
if n == 0:
for p in range(4):
c = copy.copy(base)
c.insert(p, 'E')
five_taxon_newick = '(%s);' % ','.join(c)
self.dofour_five_compat(four_taxon_newick, five_taxon_newick)
elif n == 1:
for p in range(3):
c = copy.copy(base)
sisters = [base[p], 'E']
for q in [0,1]:
c[p] = '(%s,%s)' % (sisters[q], sisters[1-q])
five_taxon_newick = '(%s);' % ','.join(c)
self.dofour_five_compat(four_taxon_newick, five_taxon_newick)
elif n == 2:
sc = copy.copy(clades)
for p in range(3):
upc = copy.copy(four_sisters)
upc.insert(p, 'E')
sc[2] = '(%s)' % ','.join(upc)
nsc = [sc[ii], sc[jj], sc[kk]]
five_taxon_newick = '(%s);' % ','.join(nsc)
self.dofour_five_compat(four_taxon_newick, five_taxon_newick)
else:
for p in range(2):
for q in range(2):
upc = copy.copy(four_sisters)
s = upc[p]
ns = [s, 'E']
upc[p] = '(%s,%s)' % (ns[q], ns[1-q])
for r in range(2):
third = '(%s,%s)' % (upc[r], upc[1-r])
nc = [clades[0], clades[1], third]
five_taxon_newick = '(%s);' % ','.join(nc)
self.dofour_five_compat(four_taxon_newick, five_taxon_newick)
BEGIN TAXA;
DIMENSIONS NTAX=5;
TAXLABELS
A
B
C
D
E
;
END;
begin trees;
tree true=(A:0.25,(B:0.25,(C:0.25,(D:0.25,E:0.25):0.25):0.25):0.25):0.25;
end;
"""
if runlevel.is_test_enabled(runlevel.SLOW, _LOG, __name__, "skipping all sequence generation frequency checking"):
class SeqSimTest(unittest.TestCase):
def setUp(self):
self.tree_model = dendropy.Tree.get_from_string(tree_model_string, schema="NEXUS")
assert self.tree_model.taxon_set is not None
def estimate_params(self,
seq_len=10000,
kappa=1.0,
base_freqs=[0.25, 0.25, 0.25, 0.25],
unequal_base_freqs=True,
gamma_rates=False,
prop_invar=False):
def testSimple(self):
if not is_test_enabled(runlevel.SLOW,
_LOG,
module_name=__name__,
message="skipping all rotation scm tests"):
return
clades = ['A', 'D', None, None]
for m in [0, 1]:
four_sisters = ['B', 'C']
clades[2] = '(%s,%s)' % (four_sisters[m], four_sisters[1 - m])
for i in [0, 1, 2]:
for j in [0, 1, 2]:
if i == j:
continue
k = [0, 1, 2]
k.remove(i)
k.remove(j)
k = k[0]
base = [clades[i], clades[j], clades[k]]
four_taxon_newick = '(%s);' % ','.join(base)
for ii in [0, 1, 2]:
for jj in [0, 1, 2]:
if ii == jj:
continue
kk = [0, 1, 2]
kk.remove(ii)
kk.remove(jj)
kk = kk[0]
base = [clades[ii], clades[jj], clades[kk]]
for n in range(4):
if n == 0:
for p in range(4):
c = copy.copy(base)
c.insert(p, 'E')
five_taxon_newick = '(%s);' % ','.join(
c)
self.dofour_five_compat(
four_taxon_newick,
five_taxon_newick)
elif n == 1:
for p in range(3):
c = copy.copy(base)
sisters = [base[p], 'E']
for q in [0, 1]:
c[p] = '(%s,%s)' % (sisters[q],
sisters[1 - q])
five_taxon_newick = '(%s);' % ','.join(
c)
self.dofour_five_compat(
four_taxon_newick,
five_taxon_newick)
elif n == 2:
sc = copy.copy(clades)
for p in range(3):
upc = copy.copy(four_sisters)
upc.insert(p, 'E')
sc[2] = '(%s)' % ','.join(upc)
nsc = [sc[ii], sc[jj], sc[kk]]
five_taxon_newick = '(%s);' % ','.join(
nsc)
self.dofour_five_compat(
four_taxon_newick,
five_taxon_newick)
else:
for p in range(2):
for q in range(2):
upc = copy.copy(four_sisters)
s = upc[p]
ns = [s, 'E']
upc[p] = '(%s,%s)' % (ns[q],
ns[1 - q])
for r in range(2):
third = '(%s,%s)' % (
upc[r], upc[1 - r])
nc = [
clades[0], clades[1], third
]
five_taxon_newick = '(%s);' % ','.join(
nc)
self.dofour_five_compat(
four_taxon_newick,
five_taxon_newick)
