def test_is_member(self):
"""Check simple set membership logic."""
self.assertTrue(
is_member(self.g, [self.pedigree.node_of[126251]]), "Should have been in genotyped list but is not"
)
self.assertFalse(is_member(self.g, [-1]), "Should have not been in genotyped list but is")
self.assertTrue(has_at_least_n_members(set([1, 2, 3]), [1, 2], 1))
self.assertTrue(has_at_least_n_members(set([1, 2, 3]), [1, 2], 2))
self.assertTrue(has_at_least_n_members(set([1, 2, 3]), [1, 2], 3))
def test_is_member(self):
'''Check simple set membership logic.'''
self.assertTrue(is_member(self.g, [self.pedigree.node_of[126251]]),
'Should have been in genotyped list but is not')
self.assertFalse(is_member(self.g, [-1]),
'Should have not been in genotyped list but is')
self.assertTrue(has_at_least_n_members(set([1, 2, 3]), [1, 2], 1))
self.assertTrue(has_at_least_n_members(set([1, 2, 3]), [1, 2], 2))
self.assertTrue(has_at_least_n_members(set([1, 2, 3]), [1, 2], 3))
def __in_extended_family(p, g, x, min_children=None):
"""Check whether a member x of a genotyped-person list g in is in a nuclear family or not according
to the pedigree graph p.
This is defined as:
CASE 1: x's parents are in G and all their children are in G;
OR
CASE 2: x has children, they are all in G and all their parents are in G.
If min_children is specified (not None), the following alternative definition is used instead:
CASE 1: x's parents are in G and at least min_children of their children are in G;
OR
CASE 2: x has children, of which at least min_children are in G; all of x's children's parents are in G.
Note: this code does not treat polygamous families correctly and assumes that such families are
'extended', i.e., have more than 2 parents.
"""
# Optimization: don't bother checking further if x is not in G
if not p.has_node(x):
raise Exception("Node " + str(x) + " not in pedigree")
if not is_member(g, [x]):
return False
# Case 1
parents = p.predecessors(x)
if is_member(g, parents) and has_at_least_n_members(g, pt.all_successors(p, parents), min_children):
return True
# Case 2
children = p.successors(x)
if (
children
and has_at_least_n_members(g, children, min_children)
and is_member(g, pt.all_predecessors(p, children))
):
return True
return False
def __in_extended_family(p, g, x, min_children=None):
'''Check whether a member x of a genotyped-person list g in is in a nuclear family or not according
to the pedigree graph p.
This is defined as:
CASE 1: x's parents are in G and all their children are in G;
OR
CASE 2: x has children, they are all in G and all their parents are in G.
If min_children is specified (not None), the following alternative definition is used instead:
CASE 1: x's parents are in G and at least min_children of their children are in G;
OR
CASE 2: x has children, of which at least min_children are in G; all of x's children's parents are in G.
Note: this code does not treat polygamous families correctly and assumes that such families are
'extended', i.e., have more than 2 parents.
'''
# Optimization: don't bother checking further if x is not in G
if not p.has_node(x):
raise Exception('Node ' + str(x) + ' not in pedigree')
if not is_member(g, [x]):
return False
# Case 1
parents = p.predecessors(x)
if (is_member(g, parents) and has_at_least_n_members(
g, pt.all_successors(p, parents), min_children)):
return True
# Case 2
children = p.successors(x)
if (children and has_at_least_n_members(g, children, min_children)
and is_member(g, pt.all_predecessors(p, children))):
return True
return False
