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#!/usr/bin/env python
#file test_birth_death.py
"""Unit tests of birth_death.py: implementation of the birth-death model.
"""
from cogent.seqsim.birth_death import ExtinctionError, TooManyTaxaError, \
BirthDeathModel, DoubleBirthDeathModel
from cogent.util.unit_test import TestCase, main, FakeRandom
__author__ = "Rob Knight"
__copyright__ = "Copyright 2007-2012, The Cogent Project"
__credits__ = ["Rob Knight", "Mike Robeson"]
__license__ = "GPL"
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
class BirthDeathModelTests(TestCase):
"""Tests of the BirthDeathModel class, which makes birth-death trees."""
def test_init_deafults(self):
"""BirthDeathModel should init correctly w/ default params"""
m = BirthDeathModel(0.1, 0.2, 0.3)
self.assertEqual(m.BirthProb, 0.1)
self.assertEqual(m.DeathProb, 0.2)
self.assertEqual(m.TimePerStep, 0.3)
self.assertEqual(m.MaxStep, 1000)
self.assertEqual(m.MaxTaxa, None)
self.assertEqual(m.CurrStep, 0)
self.assertEqual(m.Tree.__class__, m.NodeClass)
self.assertEqual(m.CurrTaxa, [m.Tree])
self.assertEqual(m.ChangedBirthProb,None)
self.assertEqual(m.ChangedDeathProb,None)
self.assertEqual(m.ChangedBirthStep,None)
self.assertEqual(m.ChangedDeathStep,None)
self.assertEqual(m.CurrBirthProb, 0.1)
self.assertEqual(m.CurrDeathProb, 0.2)
def test_init_bad(self):
"""BirthDeathModel should raise exceptions on init with bad data"""
#BirthProb and DeathProb must be probabilities between 0 and 1
self.assertRaises(ValueError, BirthDeathModel, -1, 0.2, 0.3)
self.assertRaises(ValueError, BirthDeathModel, 2, 0.2, 0.3)
self.assertRaises(ValueError, BirthDeathModel, 0.1, -1, 0.3)
self.assertRaises(ValueError, BirthDeathModel, 0.1, 2, 0.3)
#TimePerStep can't be negative or 0
self.assertRaises(ValueError, BirthDeathModel, 0.1, 0.2, -1)
self.assertRaises(ValueError, BirthDeathModel, 0.1, 0.2, 0)
def test_init_extras(self):
"""BirthDeathModel should init OK with extra params"""
m = BirthDeathModel(BirthProb=0.1, DeathProb=0.2, TimePerStep=0.3, \
ChangedBirthProb=0.4, ChangedDeathProb=0.3, ChangedBirthStep=3,\
ChangedDeathStep=4, MaxStep=5, MaxTaxa=10)
self.assertEqual(m.BirthProb, 0.1)
self.assertEqual(m.DeathProb, 0.2)
self.assertEqual(m.TimePerStep, 0.3)
self.assertEqual(m.ChangedBirthProb, 0.4)
self.assertEqual(m.ChangedDeathProb, 0.3)
self.assertEqual(m.ChangedBirthStep, 3)
self.assertEqual(m.ChangedDeathStep, 4)
self.assertEqual(m.MaxStep, 5)
self.assertEqual(m.MaxTaxa, 10)
self.assertEqual(m.CurrStep, 0)
self.assertEqual(m.Tree.__class__, m.NodeClass)
self.assertEqual(m.CurrTaxa, [m.Tree])
def test_step(self):
"""BirthDeathModel step should match hand-calculated results"""
m = BirthDeathModel(BirthProb=0.1, DeathProb=0.2, TimePerStep=1)
born_and_died = FakeRandom([0],True)
born_only = FakeRandom([1,0],True)
died_only = FakeRandom([0,1],True)
neither = FakeRandom([1],True)
kill_alternate = FakeRandom([0,1,1,1], True)
born_alternate = FakeRandom([1,1,1,0], True)
#check that with neither birth nor death, we just continue
m.step(neither)
self.assertEqual(len(m.Tree.Children), 0)
#check that with born_only we get a duplication
m.step(born_only)
self.assertEqual(len(m.Tree.Children), 2)
assert m.Tree not in m.CurrTaxa
for i in m.CurrTaxa:
assert i.Parent is m.Tree
self.assertEqual(i.Length, 1)
#check that with a second round of born_only we duplicate again
m.step(born_only)
self.assertEqual(len(m.Tree.Children), 2)
self.assertEqual(len(list(m.Tree.traverse())), 4)
for i in m.Tree.traverse():
self.assertEqual(i.Length, 1)
for i in m.Tree.Children:
self.assertEqual(i.Length, 1)
#check that branch lengths add correctly
for i in range(4):
m.step(neither)
self.assertEqual(len(m.CurrTaxa), 4)
self.assertEqual(len(m.Tree.Children), 2)
self.assertEqual(len(list(m.Tree.traverse())), 4)
for i in m.Tree.traverse():
self.assertEqual(i.Length, 5)
for i in m.Tree.Children:
self.assertEqual(i.Length, 1)
#check that we can kill offspring correctly
m.step(kill_alternate)
self.assertEqual(len(m.CurrTaxa), 2)
#make sure we killed the right children
m.Tree.assignIds()
for i in m.Tree.Children:
#note that killing a child doesn't remove it, just stops it changing
self.assertEqual(len(i.Children), 2)
self.assertEqual(i.Children[0].Length, 5)
self.assertEqual(i.Children[1].Length, 6)
self.assertEqual([i.Length for i in m.Tree.traverse()], \
[5,6,5,6])
#make sure that born_and_died does the same thing as neither
m.step(born_and_died)
self.assertEqual([i.Length for i in m.Tree.traverse()], \
[5,7,5,7])
m.step(neither)
self.assertEqual([i.Length for i in m.Tree.traverse()], \
[5,8,5,8])
#check that only CurrTaxa are brought forward
self.assertEqual([i.Length for i in m.CurrTaxa], [8,8])
#check that we can duplicate a particular taxon
m.step(born_alternate)
self.assertEqual([i.Length for i in m.CurrTaxa], [9,1,1])
self.assertEqual(m.CurrTaxa[1].Parent.Length, 8)
#check that we can kill 'em all
m.step(died_only)
self.assertEqual(len(m.CurrTaxa), 0)
def test_prob_step_check(self):
"""prob_check and step_check should return error when out of bounds.
Prob values should be between zero and one
Step values should be greater than zero
"""
#ChangedBirthProb = -0.1 , raises ValueError
self.assertRaises(ValueError, BirthDeathModel, 0.1, 0.2, 0.3,\
ChangedBirthProb=-0.1,ChangedBirthStep=3,ChangedDeathProb=0.3,\
ChangedDeathStep=4, MaxStep=5)
#ChangedBirthStep = 0 , raises ValueError
self.assertRaises(ValueError, BirthDeathModel, 0.1, 0.2, 0.3,\
ChangedBirthProb=0.6,ChangedBirthStep=0,ChangedDeathProb=0.3,\
ChangedDeathStep=4, MaxStep=5)
#ChangedDeathProb = 2 , raises ValueError
self.assertRaises(ValueError, BirthDeathModel, 0.1, 0.2, 0.3,\
ChangedBirthProb=0.6,ChangedBirthStep=3,ChangedDeathProb=2,\
ChangedDeathStep=4, MaxStep=5)
#ChangedDeathStep = -1 , raises ValueError
self.assertRaises(ValueError, BirthDeathModel, 0.1, 0.2, 0.3,\
ChangedBirthProb=0.6,ChangedBirthStep=3,ChangedDeathProb=0.3,\
ChangedDeathStep=-1, MaxStep=5)
def test_timeOk(self):
"""BirthDeathModel TimeOk should return True if time not exceeded"""
b = BirthDeathModel(0.1, 0.2, 0.3, MaxStep=5)
assert b.timeOk()
b.CurrStep = 4
assert b.timeOk()
b.CurrStep = 5
assert not b.timeOk()
b.CurrStep = 1000
assert not b.timeOk()
b.MaxStep = None
assert b.timeOk()
b.MaxStep = 1001
assert b.timeOk()
b.step()
assert not b.timeOk()
def test_taxaOk(self):
"""BirthDeathModel TaxaOk should return True if taxa not exceeded"""
b = BirthDeathModel(0.1, 0.2, 0.3, MaxTaxa=5)
born_alternate = FakeRandom([1,1,1,0], True)
born_only = FakeRandom([1,0],True)
kill_only = FakeRandom([0,1,0,1], True)
#start off with single taxon
assert b.taxaOk()
#taxa are OK if there are a few
b.step(born_only) #now 2 taxa
assert b.taxaOk()
b.step(born_only) #now 4 taxa
assert b.taxaOk()
b.step(born_only) #now 8 taxa
assert not b.taxaOk()
b.MaxTaxa = 8
assert not b.taxaOk()
b.MaxTaxa = 9
assert b.taxaOk()
b.MaxTaxa = 17
assert b.taxaOk()
b.step(born_only)
assert b.taxaOk()
b.step(born_only)
assert not b.taxaOk()
#ok if no maximum
b.MaxTaxa = None
assert b.taxaOk()
#not ok if there are no taxa left
b.step(kill_only)
assert not b.taxaOk()
#still not OK if not MaxTaxa
b.MaxTaxa = None
assert not b.taxaOk()
def test_call_exact(self):
"""BirthDeathModel call should produce right # taxa when exact"""
m = BirthDeathModel(0.01, 0.005, 0.1, MaxTaxa=10)
for i in range(10):
try:
result = m(filter=True, exact=True)
self.assertEqual(len(list(result.traverse())), 10)
except (TooManyTaxaError, ExtinctionError), e:
pass
def test_call(self):
"""BirthDeathModel call should produce hand-calculated trees"""
m = BirthDeathModel(0.01, 0.005, 0.1, MaxTaxa=10)
r = FakeRandom(\
[1,0,\
1,1, 1,1,\
1,0, 0,0,\
0,0, 0,0, 1,0,\
0,0, 0,0, 0,1, 0,0, \
1,0, 0,0, 0,0,\
1,0, 0,0, 0,0, 1,0, \
1,0, 1,0, 0,1, 1,1, 1,0, 1,0, \
1,1, 1,1, 1,1, 1,1, 1,0, 1,1, 1,1, 1,1, 1,1], True)
m = BirthDeathModel(0.1, 0.5, 1, MaxTaxa=10)
result = m(filter=False, random_f=r)
self.assertEqual([i.Length for i in result.traverse()], \
[2,2,2,2,2,1,1,1,2,2,2,2])
#try it with pruning
m = BirthDeathModel(0.1, 0.5, 1, MaxTaxa=10)
result = m(filter=True, random_f=r)
self.assertEqual([i.Length for i in result.traverse()], \
[2,2,2,2,1,1,2,2,2,2])
#try it with fewer taxa
m = BirthDeathModel(0.1, 0.5, 1, MaxTaxa=4)
result = m(filter=True, random_f=r)
self.assertEqual([i.Length for i in result.traverse()], \
[2,2,1,1])
def test_changed_values_step(self):
"""Tests if values changed at specified steps in step().
Note, in m.step() CurrStep is logically tested one step later.
"""
m = BirthDeathModel( 0.1, 0.2, 0.3,ChangedBirthProb=0.6,\
ChangedBirthStep=3,ChangedDeathProb=0.3,ChangedDeathStep=4,\
MaxStep=5)
# all values should be as initialized
m.step()
assert m.CurrStep == 1
assert m.BirthProb == 0.1
assert m.DeathProb == 0.2
assert m.CurrBirthProb == 0.1
assert m.CurrDeathProb == 0.2
# continue 2 steps
m.step()
m.step()
# when logically evaluated CurrBirthProb should change
# from 0.1 to 0.6
m.step()
assert m.CurrStep == 4
assert m.BirthProb == 0.1
assert m.DeathProb == 0.2
assert m.CurrBirthProb == 0.6
assert m.CurrDeathProb == 0.2
# All values other than CurrStep should be as above
# except that CurrDeathProb should change from 0.2 to 0.3
m.step()
assert m.CurrStep == 5
assert m.BirthProb == 0.1
assert m.DeathProb == 0.2
assert m.CurrBirthProb == 0.6
assert m.CurrDeathProb == 0.3
class DoubleBirthDeathTests(TestCase):
"""Tests of the double birth-death model."""
def test_double_birth_death(self):
"""double_birth_death should run without errors"""
pass
if __name__ == "__main__":
main()
|
