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_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 __init__(self,
famid,
name,
pid,
fathid,
mothid,
target="0",
dead="0",
age="0",
yob="0",
ashkn="0",
mztwin="0",
cancers=Cancers(),
gtests=BWSGeneticTests.default_factory(),
pathology=PathologyTest.factory_default()):
"""
@type famid: str
@param famid: family/pedigree ID
@type pid: str
@param pid: person ID
@type fathid: str
@keyword fathid: father ID
@type mothid: str
@keyword mothid: mother ID
@type target: str
@keyword target: subject of risk calculation
@type dead: str
@keyword dead: alive specified as '0' and dead as '1'
@type age: str
@keyword age: age at last follow up or age at death
@type yob: str
@keyword yob: year of birth
@type ashkn: str
@keyword ashkn: Ashkenazi origin parameter: '1' for Ashkenazi origin else '0'
@type mztwin: str
@keyword mztwin: monozygotic (identical) twin
@type cancers: Cancers
@keyword cancers: cancer status
@type gtest: GeneticTests
@keyword gtest: genetic tests
@type pathology: PathologyResult
@keyword pathology: pathology test results
"""
self.famid = famid.replace(
"-", "")[:8] # remove hyphen and restrict to 8 chars
self.name = name[:8]
self.pid = pid
self.fathid = fathid
self.mothid = mothid
self.target = target
self.dead = dead
self.age = age
self.yob = yob
self.ashkn = ashkn
self.mztwin = mztwin
self.cancers = cancers # cancers
self.gtests = gtests # genetic tests
self.pathology = pathology
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 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 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 _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])
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 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.")
def convert2csv(filename, csvfilename, censoring_ages_freq=[1, 5, 10]):
'''
Convert pedigree file to a CSV file for batch processing
@param filename - pedigree file name
@param csvfilename - name of output CSV file
@param censoring_ages - object of risk factors (e.g args.height)
'''
with open(filename, 'r') as f:
pedigree_data = f.read()
f.close()
pf = PedigreeFile(pedigree_data)
cheaders = get_rf_values(pedigree_data)
genes = Genes.get_all_model_genes()
hdr = [
"FamID", "Name", "Proband", "IndivID", "FathID", "MothID", "Sex",
"MZtwin", "Dead", "Age", "Yob", "BrCa_1st", "BrCa_2nd", "OvCa",
"ProCa", "PanCa", "Ashkn"
]
for gene in genes:
hdr.extend([gene + "t", gene + "r"])
hdr.extend(["ER", "PR", "HER2", "CK14", "CK56", "Censoring_Age"])
hdr += RISK_FACTORS # add risk factors to the header
csv_file = open(csvfilename, "w")
for i in range(len(hdr)):
print(hdr[i], file=csv_file, end="," if i < len(hdr) - 1 else "")
print('', file=csv_file)
for ped in pf.pedigrees:
trgt = ped.get_target()
tage = int(trgt.age)
alf = tage
calc_ages = []
while alf <= 79:
alf += 1
if (alf - tage in censoring_ages_freq):
calc_ages.append(str(alf))
calc_ages.append("80")
for censoring_age in calc_ages:
for person in ped.people:
print(person.famid + ":" + censoring_age,
file=csv_file,
end=",")
print(person.name, file=csv_file, end=",")
print(person.target if person.target == "1" else "",
file=csv_file,
end=",")
print(person.pid, file=csv_file, end=",")
print(person.fathid if person.fathid != "0" else "",
file=csv_file,
end=",")
print(person.mothid if person.mothid != "0" else "",
file=csv_file,
end=",")
print(person.sex(), file=csv_file, end=",")
print(person.mztwin if person.mztwin != "0" else "",
file=csv_file,
end=",")
print(person.dead, file=csv_file, end=",")
print(person.age, file=csv_file, end=",")
print(person.yob if person.yob != "0" else "",
file=csv_file,
end=",")
cancers = person.cancers
d = cancers.diagnoses
age = ""
[
print((getattr(d, c).age if getattr(d, c).age != 'AU'
and getattr(d, c).age != '-1' else age),
file=csv_file,
end=",") for c in Cancers.get_cancers()
]
print(person.ashkn, file=csv_file, end=",")
gtests = person.gtests
for g in genes:
try:
gt = getattr(gtests, g.lower())
print(gt.test_type if gt.test_type != "0" else "",
file=csv_file,
end=",")
print(gt.result if gt.result != "0" else "",
file=csv_file,
end=",")
except AttributeError:
raise
p = person.pathology
print(p.er.result if p.er.result != "0" else "",
file=csv_file,
end=",")
print(p.pr.result if p.pr.result != "0" else "",
file=csv_file,
end=",")
print(p.her2.result if p.her2.result != "0" else "",
file=csv_file,
end=",")
print(p.ck14.result if p.ck14.result != "0" else "",
file=csv_file,
end=",")
print(p.ck56.result if p.ck56.result != "0" else "",
file=csv_file,
end=",")
print((censoring_age if person.target == "1" else ""),
file=csv_file,
end="")
this_rfs = None
if person.famid in cheaders:
this_rfs = cheaders[person.famid]
for rf in RISK_FACTORS:
if person.target == "1":
if this_rfs is not None:
if rf in this_rfs:
print("," + this_rfs[rf],
file=csv_file,
end="")
else:
print(",", file=csv_file, end="")
else:
print(",", file=csv_file, end="")
else:
print(",", file=csv_file, end="")
print('', file=csv_file)
csv_file.close()
