def test_pathfraternity():
from pydigree.paths import fraternity
peds = getpeds()
ped = peds["fullsib"]
# None should return 0
assert fraternity(ped["1"], None) == 0
# Unrelated founders
assert fraternity(ped["1"], ped["2"]) == 0
# Full-sib
assert fraternity(ped["3"], ped["4"]) == 1 / 4
# Parent-child
assert fraternity(ped["1"], ped["3"]) == 0
ped = peds["first_cousins"]
# First cousins
assert fraternity(ped["7"], ped["8"]) == 0
# Avuncular (related)
assert fraternity(ped["7"], ped["5"]) == 0
# Avuncular (marry-in)
assert fraternity(ped["7"], ped["6"]) == 0
# Grandparent
assert fraternity(ped["7"], ped["1"]) == 0
ped = peds["half_sibs"]
assert fraternity(ped["4"], ped["5"]) == 0
def fraternity(self, id1, id2):
"""
Like Pedigree.kinship, this is a convenience function for getting
fraternity coefficients for two pedigree memebers by their ID label.
This is a wrapper for paths.fraternity
Returns: a double
"""
pair = frozenset([id1, id2])
if pair not in self.fratmat:
f = fraternity(self[id1], self[id2])
self.fratmat[pair] = f
return f
else:
return self.fratmat[pair]
def fraternity(self, id1, id2):
"""
Like Pedigree.kinship, this is a convenience function for getting
fraternity coefficients for two pedigree memebers by their ID label.
This is a wrapper for paths.fraternity
:param id1: the label of a individual to be evaluated
:param id2: the label of a individual to be evaluated
:returns: coefficient of fraternity
:rtype: float
"""
pair = frozenset([id1, id2])
if pair not in self.fratmat:
f = f = fraternity(self[id1], self[id2])
self.fratmat[pair] = f
return f
else:
return self.fratmat[pair]
