def test_bws_model_err(self):
''' Test ModelError raised because of pedigree file with only one twin. '''
target = Female("FAM1", "F0", "001", "002", "003", target="1", age="20", mztwin="1",
yob=str(date.today().year-20), gtests=CanRiskGeneticTests.default_factory())
pedigree = CanRiskPedigree(people=[target])
with self.assertRaisesRegex(ModelError, r"ERRORS IN THE PEDIGREE FILE"):
Predictions(pedigree)
def test_calcs_validation_err(self):
""" Test invalid calculation type raise ValidationError. """
target = Female("FAM1", "F0", "001", "002", "003", target="1", age="20",
yob=str(date.today().year-20), gtests=CanRiskGeneticTests.default_factory())
pedigree = CanRiskPedigree(people=[target])
with self.assertRaisesRegex(ValidationError, r"Unknown calculation requested: dribble"):
Predictions(pedigree, model_settings=settings.OC_MODEL, calcs=['dribble'])
def setUp(self):
''' Build pedigree data. '''
self.year = date.today().year
target = Female("FAM1", "F0", "001", "002", "003", target="1", age="20",
yob=str(self.year-20), cancers=Cancers())
self.pedigree = BwaPedigree(people=[target])
# parents
(_father, _mother) = self.pedigree.add_parents(target)
self.cwd = tempfile.mkdtemp(prefix="TEST_", dir="/tmp")
def test_mztwin_parents(self):
""" Check if an error is raised if MZ twin have different parents. """
pedigree_file = deepcopy(self.pedigree_file)
pedigree = pedigree_file.pedigrees[0]
m2 = pedigree.get_person_by_name('M2')
self._add_twin(pedigree, twin=m2)
m2.mothid = "313"
pedigree.people.append(Female(m2.famid, "F3A", "313", "0", "0"))
with self.assertRaisesRegex(PedigreeError,
r"MZ twins must have the same parents"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_father_sex(self):
''' Test an error is raised if the sex of the father is not 'M'. '''
# change sex of father to 'F'
pedigree_file = deepcopy(self.pedigree_file)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
pedigree_file.pedigrees[0].people.remove(m2)
pedigree_file.pedigrees[0].people.append(
Female(m2.famid, m2.name, m2.pid, m2.fathid, m2.mothid))
with self.assertRaisesRegex(
PersonError,
r"All fathers in the pedigree must have sex specified as 'M'"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_niceness(self):
""" Test niceness level for pedigree with sibling and large pedigree. """
pedigree = deepcopy(self.pedigree)
self.assertEqual(Predictions._get_niceness(pedigree, factor=1), len(pedigree.people))
self.assertEqual(Predictions._get_niceness(pedigree, factor=0.01), 19)
# sister
target = pedigree.get_target()
sister = Female("FAM1", "F01", "0011", target.fathid, target.mothid, age="22",
yob=str(self.year-23), cancers=Cancers(bc1=Cancer("20")))
pedigree.people.append(sister)
self.assertEqual(Predictions._get_niceness(pedigree), 1)
def setUp(self):
''' Build pedigree data. '''
self.year = date.today().year
target = Female("FAM1",
"F0",
"001",
"002",
"003",
target="1",
age="20",
yob=str(self.year - 20),
cancers=Cancers())
self.pedigree = BwaPedigree(people=[target])
# parents
(_father, _mother) = self.pedigree.add_parents(target)
# canrisk pedigree
target = Female("FAM1",
"F0",
"001",
"002",
"003",
target="1",
age="20",
yob=str(self.year - 20),
cancers=Cancers(),
gtests=CanRiskGeneticTests.default_factory())
self.canrisk_pedigree = CanRiskPedigree(people=[target])
(_father, _mother) = self.canrisk_pedigree.add_parents(
target, gtests=CanRiskGeneticTests.default_factory())
_mother.yob = str(self.year - 55)
_mother.age = "55"
_mother.cancers = Cancers(bc1=Cancer("54"),
bc2=Cancer("55"),
oc=Cancer(),
prc=Cancer(),
pac=Cancer())
self.cwd = tempfile.mkdtemp(prefix="TEST_", dir="/tmp")
def _get_pedi(self):
t = self.predictions.pedi.get_target()
if t.cancers.is_cancer_diagnosed():
cancers = Cancers(bc1=Cancer(t.cancers.diagnoses.bc1.age),
bc2=Cancer(),
oc=Cancer(),
prc=Cancer(),
pac=Cancer())
else:
cancers = Cancers()
if self.predictions.model_settings['NAME'] == 'BC':
gtests = BWSGeneticTests.default_factory()
else:
gtests = CanRiskGeneticTests.default_factory()
if t.sex() is "M":
new_t = Male(t.famid,
t.name,
t.pid,
"",
"",
target=t.target,
dead="0",
age=t.age,
yob=t.yob,
cancers=cancers,
gtests=gtests)
else:
new_t = Female(t.famid,
t.name,
t.pid,
"",
"",
target=t.target,
dead="0",
age=t.age,
yob=t.yob,
cancers=cancers,
gtests=gtests)
if self.predictions.model_settings['NAME'] == 'BC':
return BwaPedigree(people=[new_t])
else:
return CanRiskPedigree(people=[new_t])
def _add_twin(self, pedigree, twin=None, twin_key="1"):
""" Utility for creating a twin given a person in a pedigree. """
if twin is None:
twin = pedigree.get_person_by_name('M2')
twin.mztwin = twin_key
twin.fathid = "311"
twin.mothid = "312"
pedigree.people.append(Male(twin.famid, "M3", "311", "0", "0"))
pedigree.people.append(Female(twin.famid, "F3", "312", "0", "0"))
pedigree.people.append(
Male(twin.famid,
"M2A",
"111",
"311",
"312",
mztwin=twin_key,
age=twin.age,
yob=twin.yob,
gtests=deepcopy(twin.gtests),
cancers=deepcopy(twin.cancers)))
def _get_pedi(self):
t = super()._get_pedi().get_target()
cancers = Cancers()
if self.predictions.model_settings['NAME'] == 'BC':
gtests = BWSGeneticTests.default_factory()
else:
gtests = CanRiskGeneticTests.default_factory()
if t.sex() is "M":
new_t = Male(t.famid, t.name, t.pid, "", "", target=t.target,
dead="0", age=t.age, yob=t.yob, cancers=cancers,
gtests=gtests)
else:
new_t = Female(t.famid, t.name, t.pid, "", "", target=t.target,
dead="0", age=t.age, yob=t.yob, cancers=cancers,
gtests=gtests)
if self.predictions.model_settings['NAME'] == 'BC':
return BwaPedigree(people=[new_t])
else:
return CanRiskPedigree(people=[new_t])
def test_mztwin_sex(self):
""" Check if an error is raised if MZ twins are not the same sex. """
pedigree_file = deepcopy(self.pedigree_file)
pedigree = pedigree_file.pedigrees[0]
m2 = pedigree.get_person_by_name('M2')
self._add_twin(pedigree, twin=m2)
pedigree_file.pedigrees[0].people.remove(m2)
pedigree_file.pedigrees[0].people.append(
Female(m2.famid,
m2.name,
m2.pid,
m2.fathid,
m2.mothid,
mztwin=m2.mztwin,
age=m2.age,
yob=m2.yob,
cancers=m2.cancers))
with self.assertRaisesRegex(PedigreeError,
r"MZ twins must have the same sex"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_ovarian_calculations(self):
""" Test prediction of cancer risk and mutation probability. """
target = Female("FAM1",
"F0",
"001",
"002",
"003",
target="1",
age="20",
yob=str(self.year - 20),
cancers=Cancers(),
gtests=CanRiskGeneticTests.default_factory())
pedigree = CanRiskPedigree(people=[target])
# parents
(_father, _mother) = pedigree.add_parents(
target, gtests=CanRiskGeneticTests.default_factory())
PedigreeFile.validate(pedigree)
params = ModelParams(
mutation_frequency=settings.OC_MODEL['MUTATION_FREQUENCIES']["UK"],
mutation_sensitivity=settings.OC_MODEL['GENETIC_TEST_SENSITIVITY'])
calcs = Predictions(pedigree,
cwd=self.cwd,
model_params=params,
model_settings=settings.OC_MODEL,
calcs=[])
# each gene should have a mutation probability plus a result for no mutations
for mp in calcs.mutation_probabilties:
key = list(mp.keys())[0]
self.assertTrue(key in settings.OC_MODEL['GENES']
or key == "no mutation")
self.assertEqual(len(calcs.mutation_probabilties),
len(settings.OC_MODEL['GENES']) + 1)
# risks calculated at 16 different ages:
self.assertEqual(len(calcs.cancer_risks), 16)
self.assertTrue(
[c.get('age') for c in calcs.cancer_risks] ==
[21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80])