def test_missing_father(self):
''' Test an error is raised if the father is missing. '''
# remove father M2 from pedigree
pedigree_file = deepcopy(self.pedigree_file)
PedigreeFile.validate(pedigree_file.pedigrees)
m2 = pedigree_file.pedigrees[0].get_person_by_name('M2')
pedigree_file.pedigrees[0].people.remove(m2)
with self.assertRaisesRegex(PersonError,
r"The father (.*) is missing"):
PedigreeFile.validate(pedigree_file.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_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_result_specified(self):
""" Check that the mutation status is specified if tested. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.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(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, "\"" + f1.pid +
"\" .* genetic test type has not been specified"):
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,
m2.pid + "*. diagnosis that exceeds age at last follow up"):
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_canrisk_header(self):
''' Test canrisk file header. '''
PedigreeFile(self.canrisk_data)
canrisk_data = copy.copy(self.canrisk_data)
canrisk_data = canrisk_data.replace('CanRisk ', 'CanRisky ', 1)
with self.assertRaisesRegex(
PedigreeFileError,
r"header record in the pedigree file has unexpected characters"
):
PedigreeFile(canrisk_data)
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_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_result(self):
""" Check that the mutation status is valid. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.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(pedigree_file.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_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_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_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_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_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_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 test_multiple_pedigrees(self):
''' Test multiple pedigrees in a single file. '''
pedigree_data1 = copy.copy(self.pedigree_data)
pedigree_data2 = '\n'.join(pedigree_data1.split('\n')[2:]).replace(
"XXX", "YYY")
pedigree_data3 = pedigree_data2.replace("YYY", "ZZZ")
pedigree_data = pedigree_data1 + '\n\n' + pedigree_data2 + '\n\n' + pedigree_data3
pedigrees = PedigreeFile(pedigree_data).pedigrees
self.assertEqual(len(pedigrees), 3)
for p in pedigrees:
warnings = PedigreeFile.validate(p)
self.assertEqual(len(warnings), 0)
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)
def get_rfs(bwa):
''' Get risk factor names and values plus PRS from CanRisk file for CSV file '''
rfsnames = []
rfs = {}
f = open(bwa, "r")
for line in f:
if line.startswith(
"##") and "##CanRisk" not in line and "##FamID" not in line:
if "PRS_BC" in line: # alpha=0.45,zscore=0.1234
add_prs(line, 'BC', rfsnames, rfs)
elif "PRS_OC" in line: # alpha=0.45,zscore=0.1234
add_prs(line, 'OC', rfsnames, rfs)
else:
line = line.replace("##", "").strip().split("=")
if line[0].isupper():
if line[0] == 'TL':
name = 'Tubal_Ligation'
else:
name = line[0]
elif line[0] == 'mht_use':
name = 'MHT_use'
elif line[0] == 'height':
name = line[0]
line[1] = ("%8.4f" % float(line[1]))
elif line[0] == 'oc_use':
name = 'OC_Use'
if line[1] == "N" or line[1] == "C":
rfsnames.append(['OC_Duration', 'OC_Duration'])
rfs['OC_Duration'] = '0'
elif ":" in line[1]:
rfsnames.append(['OC_Duration', 'OC_Duration'])
parts = line[1].split(":")
rfs['OC_Duration'] = parts[1]
line[1] = parts[0]
elif line[0] == 'birads':
name = 'BIRADS'
elif line[0] == 'endo':
name = 'Endometriosis'
else:
name = line[0].capitalize()
rfsnames.append([line[0], name])
rfs[line[0]] = line[1]
f.close()
with open(bwa, 'r') as f:
pedigree_data = f.read()
pedigree = PedigreeFile(pedigree_data).pedigrees[0]
ashkn = pedigree.is_ashkn()
return rfsnames, rfs, ashkn
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_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_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_target_risk_prob_calcs(self):
""" Check if an error is raised if the carrier probabilities and cancer risk can not be
calculated.
If the target has a positive genetic test carrier probs cannot be calculated. Had bilateral
BC or OC or PanC, or she is too old. """
pedigree_file = deepcopy(self.pedigree_file)
f1 = pedigree_file.pedigrees[0].get_person_by_name('F1')
f1.gtests.brca1.result = "P"
f1.cancers.diagnoses.bc2.age = 18
with self.assertRaisesRegex(
PedigreeError,
r"cannot compute mutation carrier probabilities"):
PedigreeFile.validate(pedigree_file.pedigrees)
def get_censoring_ages(bwa):
with open(bwa, 'r') as f:
pedigree_data = f.read()
f.close()
pedigree = PedigreeFile(pedigree_data).pedigrees[0]
# get ages to calculate risks
target = pedigree.get_target()
tage = int(target.age) # target age at last follow up
c_ages = []
alf = tage
while alf <= 79:
alf += 1
if alf - tage in [1, 5, 10]:
c_ages.append(alf)
c_ages.append(80)
return c_ages
def is_canrisk(bwa):
''' Return true if CanRisk file type '''
with open(bwa, 'r') as f:
pedigree_data = f.read()
pedigree = PedigreeFile(pedigree_data).pedigrees[0]
return isinstance(pedigree, CanRiskPedigree)
def test_sex(self):
""" Test an error is raised if individuals sex is not M or F. """
pedigree_data = copy.copy(self.pedigree_data)
pedigree_data = re.sub(r"\s+F\s+", ' FF ', pedigree_data)
with self.assertRaisesRegex(PedigreeError,
r"individuals sex must be specified as"):
PedigreeFile(pedigree_data)
def test_no_target(self):
""" Test an error is raised if there is no target. """
pedigree_data = copy.copy(self.pedigree_data)
pedigree_data = re.sub(r"F1\s+1", 'F1 0', pedigree_data)
with self.assertRaisesRegex(PedigreeError,
r"has either no index or more than 1"):
PedigreeFile(pedigree_data)
