def test_siblings_same_yob(self):
""" Check max no. of siblings with same year of birth is not exceeded. """
pedigree_file = deepcopy(self.pedigree_file)
pedigree = pedigree_file.pedigrees[0]
f1 = pedigree.get_person_by_name('F1')
self.assertEqual(len(pedigree.get_siblings(f1)[1]), 0)
pedigree.people.append(
Male(f1.famid, "M1A", "111", f1.fathid, f1.mothid, yob=f1.yob))
pedigree.people.append(
Male(f1.famid, "M1B", "112", f1.fathid, f1.mothid, yob=f1.yob))
self.assertEqual(len(pedigree.get_siblings(f1)[1]), 2)
with self.assertRaisesRegex(
PersonError, r"siblings with the same year of birth exceeded"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_siblings(self):
""" Check max no. of siblings not exceeded. """
pedigree_file = deepcopy(self.pedigree_file)
pedigree = pedigree_file.pedigrees[0]
f1 = pedigree.get_person_by_name('F1')
self.assertEqual(len(pedigree.get_siblings(f1)[0]), 0)
pedigree.people.append(
Male(f1.famid, "M1A", "111", f1.fathid, f1.mothid))
pedigree.people.append(
Male(f1.famid, "M1B", "112", f1.fathid, f1.mothid))
self.assertEqual(len(pedigree.get_siblings(f1)[0]), 2)
with self.assertRaisesRegex(PersonError,
r"exeeded the maximum number of siblings"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_ununconnected(self):
pedigree_file = deepcopy(self.pedigree_file)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
pedigree_file.pedigrees[0].people.append(
Male(m2.famid, "M1A", "111", "0", "0"))
with self.assertRaisesRegex(
PedigreeError,
r"family members are not physically connected to the target"):
PedigreeFile.validate(pedigree_file.pedigrees)
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 test_mother_sex(self):
''' Test an error is raised if the sex of the mother is not 'F'. '''
# change sex of mother to 'M'
pedigree_file = deepcopy(self.pedigree_file)
f2 = pedigree_file.pedigrees[0].get_person_by_name('F2')
pedigree_file.pedigrees[0].people.remove(f2)
pedigree_file.pedigrees[0].people.append(
Male(f2.famid, f2.name, f2.pid, f2.fathid, f2.mothid))
with self.assertRaisesRegex(
PersonError,
r"All mothers in the pedigree must have sex specified as 'F'"):
PedigreeFile.validate(pedigree_file.pedigrees)
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])
