def test_mztwin_key(self):
""" Check if an error is raised if MZ twin characters are not valid. """
pedigree_file = deepcopy(self.pedigree_file)
self._add_twin(pedigree_file.pedigrees[0], twin_key="X")
with self.assertRaisesRegex(PedigreeError,
r"MZ twins must be identified using one"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_ashkn(self):
""" Test an error is raised if the Ashkenazi origin is incorrectly assigned (i.e. not 0 or 1). """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.ashkn = "x"
with self.assertRaisesRegex(PersonError, r"invalid Ashkenazi"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_type(self):
""" Check that the genetic test type is valid. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.gtests.brca1.test_type = "X"
with self.assertRaisesRegex(GeneticTestError,
"invalid genetic test type"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_female_with_prostate_cancer(self):
""" Test an error is raised if a female has been designated prostate cancer. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.cancers.diagnoses.prc.age = "21"
with self.assertRaisesRegex(
CancerError, r"female but has been assigned an prostate"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_male_with_ovarian_cancer(self):
""" Test an error is raised if a male has been designated ovarian cancer. """
pedigree_file = deepcopy(self.pedigree_file)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
m2.cancers.diagnoses.oc.age = "45"
with self.assertRaisesRegex(CancerError,
r"male but has been assigned an ovarian"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_mztwin_pair(self):
""" Check if an error is raised if the number of people specified in a set of twins is not 2. """
pedigree_file = deepcopy(self.pedigree_file)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
m2.mztwin = "1"
with self.assertRaisesRegex(
PedigreeError, r"Only MZ twins are permitted in the pedigree"):
PedigreeFile.validate(pedigree_file.pedigrees)
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_target_age(self):
""" The target must be assigned a valid year of birth. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.age = "0"
with self.assertRaisesRegex(PedigreeError,
r"This person must be assigned an age"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_mztwin_number(self):
""" Check if an error is raised if the number of people specified in a set of twins is not 2. """
pedigree_file = deepcopy(self.pedigree_file)
self._add_twin(pedigree_file.pedigrees[0])
with self.assertRaisesRegex(
PedigreeError,
r"Maximum number of MZ twin pairs has been exceeded"):
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 test_cancer_age2(self):
''' Test an error is raised if the cancer diagnosis age is greater than age at last follow up. '''
pedigree_file = deepcopy(self.pedigree_file)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
m2.cancers.diagnoses.bc1.age = "59"
m2.age = "53"
with self.assertRaisesRegex(
CancerError, r"diagnosis that exceeds age at last follow up"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_type_specified(self):
""" Check if there is a genetic test result check the test type is specified. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.gtests.brca1.test_type = "0"
f1.gtests.brca1.result = "P"
with self.assertRaisesRegex(
GeneticTestError, "genetic test type has not been specified"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_missing_mother(self):
''' Test an error is raised if the mother is missing. '''
# remove mother F2 from pedigree
pedigree_file = deepcopy(self.pedigree_file)
f2 = pedigree_file.pedigrees[0].get_person_by_name('F2')
pedigree_file.pedigrees[0].people.remove(f2)
with self.assertRaisesRegex(PersonError,
r"The mother (.*) is missing"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_name(self):
""" Test an error is raised if the individuals name is not an alphanumeric string. """
pedigree_file = deepcopy(self.pedigree_file)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
m2.name = "M<2"
with self.assertRaisesRegex(
PersonError,
r"is unspecified or is not an alphanumeric string"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_cancer_yob(self):
''' Test an error is raised if the yob is not specified when a cancer is diagnosed. '''
pedigree_file = deepcopy(self.pedigree_file)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
m2.yob = "0"
with self.assertRaisesRegex(
CancerError, m2.pid +
"*. diagnosed with cancer but has no year of birth specified"):
PedigreeFile.validate(pedigree_file.pedigrees)
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_result_specified(self):
""" Check that the mutation status is specified if tested. """
pfile = self.get_pedigree_file()
f1 = pfile.pedigrees[0].get_person_by_name('F1')
f1.gtests.brca1.test_type = "S"
f1.gtests.brca1.result = "0"
with self.assertRaisesRegex(
GeneticTestError, "\"" + f1.pid +
"\" .* corresponding test result has not been specified"):
PedigreeFile.validate(pfile.pedigrees)
def test_bc1_and_bc2(self):
""" Test an error is raised if the age of a first breast cancer exceeds that of the second. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.cancers.diagnoses.bc1.age = "22"
f1.cancers.diagnoses.bc2.age = "21"
with self.assertRaisesRegex(
CancerError, f1.pid + "*. contralateral breast cancer, (.*) " +
"age at diagnosis of the first breast cancer exceeds"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_bc1_missing2(self):
""" Test an error is raised if the age of a second breast cancer is AU but age of first is missing. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.cancers.diagnoses.bc1.age = "-1"
f1.cancers.diagnoses.bc2.age = "AU"
with self.assertRaisesRegex(
CancerError, f1.pid + "*. contralateral breast cancer, (.*) " +
"first breast cancer is missing"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_result(self):
""" Check that the mutation status is valid. """
pfile = self.get_pedigree_file()
f1 = pfile.pedigrees[0].get_person_by_name('F1')
f1.gtests.brca1.test_type = "S"
f1.gtests.brca1.result = "X"
with self.assertRaisesRegex(
GeneticTestError,
"\"" + f1.pid + "\" .* invalid genetic test result"):
PedigreeFile.validate(pfile.pedigrees)
def test_pathology_status(self):
""" Check that the pathology results are correctly set (0, N, P). """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.pathology.er.result = 'X'
with self.assertRaisesRegex(
PathologyError,
"must be 'N' for negative, 'P' for positive, or '0' for unknown"
):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_dead(self):
''' Test an error is raised if the dead attribute is incorrectly specified (not 0 or 1). '''
pedigree_file = deepcopy(self.pedigree_file)
PedigreeFile.validate(pedigree_file.pedigrees)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
m2.dead = "3"
with self.assertRaisesRegex(
PersonError,
r"alive must be specified as '0', and dead specified as '1'"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_mztwin_yob(self):
""" Check if an error is raised if MZ twin have different years of birth. """
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.yob = str(int(m2.yob) + 2)
with self.assertRaisesRegex(
PedigreeError, r"MZ twins must have the same year of birth"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_bc1_missing(self):
""" Test an error is raised if the age of a second breast cancer is present but age of first is missing. """
pfile = self.get_pedigree_file()
f1 = pfile.pedigrees[0].get_person_by_name('F1')
f1.cancers.diagnoses.bc1.age = "-1"
f1.cancers.diagnoses.bc2.age = "21"
with self.assertRaisesRegex(
CancerError,
".*\"" + f1.pid + "\".* contralateral breast cancer, (.*) " +
"first breast cancer is missing"):
PedigreeFile.validate(pfile.pedigrees)
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_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_age(self):
''' Test an error is raised if the age attribute is incorrectly specified (not 0 or 1-MAX_AGE). '''
pedigree_file = deepcopy(self.pedigree_file)
PedigreeFile.validate(pedigree_file.pedigrees)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
m2.age = "222"
with self.assertRaisesRegex(
PersonError,
r"Ages must be specified with as '0' for unknown, or in the range"
):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_patholgy_bc1_setting(self):
""" Check that pathology test results are only provided for family members with a first breast cancer """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.cancers.diagnoses.bc1.age = "-1"
f1.pathology.er.result = "P"
with self.assertRaisesRegex(
PathologyError,
"Pathology test results can only be assigned to family " +
"members who have developed breast cancer."):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_cancer_age(self):
''' Test an error is raised if the cancer diagnosis age is incorrectly specified (not 0 or 1-MAX_AGE). '''
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.cancers.diagnoses.bc1.age = "xyz"
with self.assertRaisesRegex(CancerError, r"Age at cancer diagnosis"):
PedigreeFile.validate(pedigree_file.pedigrees)
f1.cancers.diagnoses.bc1.age = "199"
with self.assertRaisesRegex(CancerError, r"Age at cancer diagnosis"):
PedigreeFile.validate(pedigree_file.pedigrees)
def test_mztwin_age(self):
""" Check if an error is raised if MZ twin are alive and have different ages at last followup. """
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.age = "44"
with self.assertRaisesRegex(
PedigreeError,
r"If both MZ twins are alive, they must have the same age at last"
):
PedigreeFile.validate(pedigree_file.pedigrees)
