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 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 _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])
class RiskTests(TestCase):
""" Calculation testing. """
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 tearDown(self):
TestCase.tearDown(self)
shutil.rmtree(self.cwd)
def test_calculations(self):
""" Test prediction of cancer risk and mutation probability. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
calcs = Predictions(pedigree, cwd=self.cwd)
# 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.BC_MODEL['GENES'] or key == "no mutation")
self.assertEqual(len(calcs.mutation_probabilties), len(settings.BC_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])
def test_calculations2(self):
""" Test prediction of cancer risk and mutation probability. """
pedigree = deepcopy(self.pedigree)
target = pedigree.get_target()
target.age = str(int(target.age) + 43)
# sister
# diagnoses = CancerDiagnoses(bc1=Cancer("20"), bc2=Cancer(), oc=Cancer(),
# prc=Cancer(), pac=Cancer())
# sister = Female("FAM1", "F01", "0011", target.fathid, target.mothid, age="22", yob=str(self.year-23),
# cancers=Cancers(diagnoses=diagnoses))
# pedigree.people.append(sister)
# parents
mother = pedigree.get_person(target.mothid)
mother.yob = str(self.year-84)
mother.age = "85"
mother.cancers = Cancers(bc1=Cancer("52"), bc2=Cancer(), oc=Cancer(), prc=Cancer(), pac=Cancer())
# maternal grandparents
(_maternal_grandfather, maternal_grandmother) = pedigree.add_parents(mother)
maternal_grandmother.age = "81"
maternal_grandmother.yob = "1912"
maternal_grandmother.dead = "1"
maternal_grandmother.cancers = Cancers(bc1=Cancer("42"), bc2=Cancer(), oc=Cancer(),
prc=Cancer(), pac=Cancer())
PedigreeFile.validate(pedigree)
calcs = Predictions(pedigree, cwd=self.cwd)
# 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.BC_MODEL['GENES'] or key == "no mutation")
self.assertEqual(len(calcs.mutation_probabilties), len(settings.BC_MODEL['GENES']) + 1)
# risks calculated at different ages:
self.assertEqual(len(calcs.cancer_risks), 9)
self.assertTrue([c.get('age') for c in calcs.cancer_risks] ==
[64, 65, 66, 67, 68, 70, 73, 75, 80])
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])
def test_lifetime_risk(self):
""" Test lifetime risk calculation matches the risk to 80 for a 20 year old. """
pedigree = deepcopy(self.pedigree)
t = pedigree.get_target()
t.age = '20'
PedigreeFile.validate(pedigree)
calcs = Predictions(pedigree, cwd=self.cwd)
c80 = None
for c in calcs.cancer_risks:
if c.get('age') == 80:
c80 = c
self.assertEqual(calcs.lifetime_cancer_risk[0]['breast cancer risk']['decimal'],
c80['breast cancer risk']['decimal'])
self.assertEqual(calcs.lifetime_cancer_risk[0]['ovarian cancer risk']['decimal'],
c80['ovarian cancer risk']['decimal'])
def test_10yr_range_risk(self):
""" Test ten year range (40-49) risk calculation matches the risk to 50 for a 40 year old. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
calcs1 = Predictions(pedigree, cwd=self.cwd)
t = pedigree.get_target()
t.age = '40'
calcs2 = Predictions(pedigree, cwd=self.cwd)
c50 = None
for c in calcs2.cancer_risks:
if c.get('age') == 50:
c50 = c
self.assertEqual(calcs1.ten_yr_cancer_risk[0]['breast cancer risk']['decimal'],
c50['breast cancer risk']['decimal'])
self.assertEqual(calcs1.ten_yr_cancer_risk[0]['ovarian cancer risk']['decimal'],
c50['ovarian cancer risk']['decimal'])
def test_pedigree_remaining_lifetime(self):
""" Test pedigree for remaining lifetime risk calculation. """
p1 = deepcopy(self.pedigree)
PedigreeFile.validate(p1)
calcs = Predictions(p1, cwd=self.cwd, run_risks=False)
self.assertTrue(calcs.pedi.is_carrier_probs_viable())
self.assertTrue(calcs.pedi.is_risks_calc_viable())
remaining_life = RemainingLifetimeRisk(calcs)
p2 = remaining_life._get_pedi()
self.assertEqual(len(p1.people), len(p2.people))
self.assertEqual(p1.get_target().age, p2.get_target().age)
def test_pedigree_range_baseline(self):
""" Test pedigree for baseline time range (e.g. lifetime, 10yr range) risk calculation. """
p1 = deepcopy(self.pedigree)
PedigreeFile.validate(p1)
calcs = Predictions(p1, cwd=self.cwd, run_risks=False)
range_baseline = RangeRiskBaseline(calcs, 40, 50, "10 YR RANGE BASELINE")
p2 = range_baseline._get_pedi()
self.assertEqual(len(p2.people), 1)
self.assertEqual(p2.get_target().age, 40)
self.assertNotEqual(p1.get_target().age, p2.get_target().age)
def test_incidence_rates(self):
""" Test prediction of cancer risk and mutation probability for different incidence rates. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
target = pedigree.get_target()
target.age = 78
crates = settings.BC_MODEL['CANCER_RATES']
for cancer_rates in crates.values():
params = ModelParams(cancer_rates=cancer_rates)
calcs = Predictions(pedigree, cwd=self.cwd, model_params=params)
# each gene should have a mutation probability plus a result for no mutations
self.assertEqual(len(calcs.mutation_probabilties), len(settings.BC_MODEL['GENES']) + 1)
# risks calculated at different ages:
self.assertTrue([c.get('age') for c in calcs.cancer_risks] ==
[79, 80])
def test_affected_unknown(self):
""" Test including affected unknown for mother of target to show it increases breast cancer risk. """
pedigree = deepcopy(self.pedigree)
target = pedigree.get_target()
mother = pedigree.get_person(target.mothid)
mother.yob = str(self.year-55)
mother.age = "55"
calcs1 = Predictions(pedigree, cwd=self.cwd)
def get_c80(calcs):
for c in calcs.cancer_risks:
if c.get('age') == 80:
return c['breast cancer risk']['decimal']
return None
# add affected unknown to mother
mother.cancers = Cancers(bc1=Cancer("AU"), bc2=Cancer(), oc=Cancer(), prc=Cancer(), pac=Cancer())
calcs2 = Predictions(pedigree, cwd=self.cwd)
self.assertGreater(get_c80(calcs2), get_c80(calcs1), 'Mother affected unknown increases BC risk in target')
def test_mutation_frequencies(self):
""" Test prediction of cancer risk and mutation probability for different mutation frequencies. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
target = pedigree.get_target()
target.age = 78
mutation_frequencies = settings.BC_MODEL['MUTATION_FREQUENCIES']
for mf in mutation_frequencies.keys():
if mf == 'Custom':
continue
params = ModelParams(mutation_frequency=mutation_frequencies[mf])
calcs = Predictions(pedigree, cwd=self.cwd, model_params=params)
# each gene should have a mutation probability plus a result for no mutations
self.assertEqual(len(calcs.mutation_probabilties), len(settings.BC_MODEL['GENES']) + 1)
# risks calculated at different ages:
self.assertTrue([c.get('age') for c in calcs.cancer_risks] ==
[79, 80])
def test_subproces_err(self):
""" Test subprocess raises an error when the fortran can not be run. """
pedigree = deepcopy(self.pedigree)
PedigreeFile.validate(pedigree)
with self.assertRaises(FileNotFoundError):
model_settings = settings.BC_MODEL
model_settings['HOME'] = 'xyz'
Predictions(pedigree, cwd=self.cwd, model_settings=model_settings)
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)