def test_generation_no_stop(self):
"""
Tests an assert is raised if no stopping criteria are given.
"""
with self.assertRaises(ValueError):
ngesh.gen_tree(1.0, 0.5)
def test_generation_seed_bio_label(self):
"""
Test equality of trees generated with the same seed, bio label.
"""
# Enumerating label
t1 = ngesh.gen_tree(1.0, 0.5, max_time=3.0, labels="bio", seed=1234)
t2 = ngesh.gen_tree(1.0, 0.5, max_time=3.0, labels="bio", seed=1234)
assert t1.write() == t2.write()
def test_generation_seed_no_label(self):
"""
Test equality of trees generated with the same seed, no label.
"""
# No label
t1 = ngesh.gen_tree(1.0, 0.5, max_time=3.0, labels=None, seed=1234)
t2 = ngesh.gen_tree(1.0, 0.5, max_time=3.0, labels=None, seed=1234)
assert t1.write() == t2.write()
def tree_test():
CONCEPTS = 10
# generate a fixed tree for the tests
tree = ngesh.gen_tree(1.0, 0.5, max_time=1.0, labels="human", seed=13)
# TODO: need to add seed to `add_characters`
# TODO: need to sort the taxa in output in `tree2nexus`
tree = ngesh.add_characters(tree, CONCEPTS, 3.0, 0.5, seed=13)
# collect all taxa and their characters, provided the characters exist
# TODO: reuse code? already in tree2nexus
data = {leaf.name: leaf.chars for leaf in tree.get_leaves()}
# get the number of words to generate -- we generate all those that
# will be used at the beginning, following their path as if they
# always existed
# TODO: generate based on phonology of current available ones?
num_words = max([max(chars) for chars in data.values()]) + 1
words = abzu.kiss.random_words(num_words, param={})
print(tree)
print(ngesh.tree2nexus(tree))
print(data)
print(words, len(words))
for node in tree.iter_descendants():
print([node.name], node.dist)
print(dir(node))
def test_generation_max_time(self):
"""
Tests tree generation with maximum_time stop criterion.
"""
tree = ngesh.gen_tree(1.0, 0.5, max_time=0.1, seed="myseed")
assert (tree.write() ==
"((L1:0.0437074,L2:0.0437074)1:0.0503426,L3:0.09405);")
def test_generation_yule_model(self):
"""
Tests tree generation in a birth-only model.
"""
tree = ngesh.gen_tree(1.0, 0.0, max_time=1.0, seed="myseed")
assert (
tree.write() ==
"((((L01:0.0210924,L02:0.0210924)1:0.114516,((L03:0.108258,L04:0.108258)1:0.0135044,(L05:0.110611,L06:0.110611)1:0.0111507)1:0.0138468)1:0.0157386,(L07:0.124442,L08:0.124442)1:0.0269054)1:0.798963,((L09:0.096708,L10:0.096708)1:0.655743,L11:0.752451)1:0.197859);"
)
def test_generation_min_leaves(self):
"""
Tests tree generation with minimum leaf number stop criterion.
"""
tree = ngesh.gen_tree(1.0, 0.5, min_leaves=5, seed="myseed")
assert (
tree.write() ==
"(L1:0.532642,((L2:0.0290176,L3:0.0290176)1:0.411228,((L4:0.0111507,L5:0.0111507)1:0.00297779,L6:0.0141285)1:0.426117)1:0.131906);"
)
def test_generation_polytomy(self):
"""
Tests tree generation with hard politomy.
"""
tree = ngesh.gen_tree(1.0, 0.5, min_leaves=25, lam=2.5, seed="myseed")
assert (
tree.write() ==
"((L01:0.278359,L02:0.267157,((L03:0.329973,L04:0.329973,L05:0.329973)1:0.00737038,L06:0.337343,L07:0.00637183,(L08:0.154122,(L09:0.286005,L10:0.286005,L11:0.286005,L12:0.108018,L13:0.010044,L14:0.286005,L15:0.03119)1:0.0378078,L16:0.323813)1:0.0135302,L17:0.337343)1:0.279476,((L18:0.127314,L19:0.127314,L20:0.127314,((L21:0.0391456,L22:0.0391456,L23:0.0391456,L24:0.0391456)1:0.026045,L25:0.0651906,L26:0.0651906)1:0.0621232,L27:0.127314)1:0.217102,L28:0.344416,L29:0.344416,L30:0.344416)1:0.272403)1:0.131906,L31:0.748725,L32:0.748725);"
)
def test_generation_pruning(self):
"""
Tests tree generation with pruning in a birth-death model.
"""
tree = ngesh.gen_tree(1.0,
0.5,
max_time=5.0,
prune=True,
seed="myseed")
assert (
tree.write() ==
"(L01:2.08229,((((L02:0.836492,(L03:0.481244,L04:0.481244)1:0.266392)1:0.256375,L05:1.09287)1:0.325198,(((L06:0.0445452,L07:0.0445452)1:0.264622,L08:0.309167)1:0.323491,L09:0.632659)1:0.297593)1:1.46117,(((L10:0.925725,(L11:0.743874,L12:0.18682)1:0.0634664)1:0.304216,L13:0.490981)1:0.0129382,L14:0.740564)1:0.385008)1:0.692202);"
)
def test_generation_labelling(self):
"""
Tests tree generation with all the label models.
"""
e_tree = ngesh.gen_tree(1.0,
0.5,
max_time=0.5,
labels="enum",
seed="myseed")
h_tree = ngesh.gen_tree(1.0,
0.5,
max_time=0.5,
labels="human",
seed="myseed")
b_tree = ngesh.gen_tree(1.0,
0.5,
max_time=0.5,
labels="bio",
seed="myseed")
assert (
e_tree.write() ==
"(L1:0.449746,((L2:0.0968117,L3:0.0968117)1:0.330426,L4:0.26938)1:0.0225083);"
)
assert (
h_tree.write() ==
"(Hifvepo:0.449746,((Bibeu:0.0968117,Pelbe:0.0968117)1:0.330426,Fuzegpu:0.26938)1:0.0225083);"
)
assert (
b_tree.write() ==
"(Sbibeus neartas:0.449746,((Spelbes rempucis:0.0968117,Spuzegpus spicus:0.0968117)1:0.330426,Wipepo uales:0.26938)1:0.0225083);"
)
# Assert error
with self.assertRaises(ValueError):
ngesh.gen_tree(1.0, 0.5, max_time=0.5, labels="XXX")
def new_tree(args):
"""
Generates and returns a new tree.
This function is a simple wrapper on the main `gen_tree()` and
`add_characters()` functions. It is intented for command-line usage,
but it can be used in code for quick prototyping.
Parameters
----------
args : Namespace
A namespace with the parameters for tree generation.
Returns
-------
tree: ete3 object
The randomly generated tree.
"""
# Generate the random tree
tree = ngesh.gen_tree(
args.birth,
args.death,
min_leaves=args.min_leaves,
max_time=args.max_time,
labels=args.labels,
lam=args.lam,
seed=args.seed,
)
# Add characters if requested
if args.num_chars:
tree = ngesh.add_characters(
tree,
args.num_chars,
args.k_mut,
args.th_mut,
k_hgt=args.k_hgt,
th_hgt=args.th_hgt,
e=args.e_mut,
seed=args.seed,
)
# Simulate bad sampling if requested
if args.sampling:
ngesh.simulate_bad_sampling(tree, args.sampling, seed=args.seed)
return tree