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_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 _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 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 factory(ped_file_line, file_type=None):
''' Factory method for creating types of people given a record from
a BOADICEA import pedigree file .
@type ped_file_line: str
@param ped_file_line: Pedigree file line.
'''
cols = ped_file_line.split()
famid = cols[0]
name = cols[1]
pid = cols[3]
cancers = Cancers(bc1=Cancer(cols[11] if cols[11] != "0" else "-1"),
bc2=Cancer(cols[12] if cols[12] != "0" else "-1"),
oc=Cancer(cols[13] if cols[13] != "0" else "-1"),
prc=Cancer(cols[14] if cols[14] != "0" else "-1"),
pac=Cancer(cols[15] if cols[15] != "0" else "-1"))
# use column headers to get gene test type and result
if file_type == 'bwa':
gtests = BWSGeneticTests.factory([
GeneticTest(cols[BwaPedigree.get_column_idx(gene + 't')],
cols[BwaPedigree.get_column_idx(gene + 'r')])
for gene in settings.BC_MODEL['GENES']
])
pathology = PathologyTests(
er=PathologyTest(PathologyTest.ESTROGEN_RECEPTOR_TEST,
cols[27]),
pr=PathologyTest(PathologyTest.PROGESTROGEN_RECEPTOR_TEST,
cols[28]),
her2=PathologyTest(PathologyTest.HER2_TEST, cols[29]),
ck14=PathologyTest(PathologyTest.CK14_TEST, cols[30]),
ck56=PathologyTest(PathologyTest.CK56_TEST, cols[31]))
else:
genes = settings.BC_MODEL['GENES'] + settings.OC_MODEL['GENES'][2:]
def get_genetic_test(cols, gene):
idx = CanRiskPedigree.get_column_idx(gene)
if idx < 0:
raise PedigreeError("Genetic test column for '" + gene +
"not found.")
gt = cols[idx].split(':')
return GeneticTest(gt[0], gt[1])
gtests = CanRiskGeneticTests.factory(
[get_genetic_test(cols, gene) for gene in genes])
path = cols[len(CanRiskPedigree.COLUMNS) - 1].split(':')
pathology = PathologyTests(
er=PathologyTest(PathologyTest.ESTROGEN_RECEPTOR_TEST,
path[0]),
pr=PathologyTest(PathologyTest.PROGESTROGEN_RECEPTOR_TEST,
path[1]),
her2=PathologyTest(PathologyTest.HER2_TEST, path[2]),
ck14=PathologyTest(PathologyTest.CK14_TEST, path[3]),
ck56=PathologyTest(PathologyTest.CK56_TEST, path[4]))
if cols[6] == 'M':
return Male(famid,
name,
pid,
fathid=cols[4],
mothid=cols[5],
target=cols[2],
dead=cols[8],
age=cols[9],
yob=cols[10],
ashkn=cols[16],
cancers=cancers,
mztwin=cols[7],
gtests=gtests,
pathology=pathology)
elif cols[6] == 'F':
return Female(famid,
name,
pid,
fathid=cols[4],
mothid=cols[5],
target=cols[2],
dead=cols[8],
age=cols[9],
yob=cols[10],
ashkn=cols[16],
cancers=cancers,
mztwin=cols[7],
gtests=gtests,
pathology=pathology)
else:
raise PedigreeError(
"The sex of family member '" + name + "' is invalid. An " +
"individuals sex must be specified as 'M' or 'F' only.")
