def test_split_disjoint(self): family, genotyped = read_ped_file(os.path.join(DATA_DIR, 'ped_soup.ped')) self.assertEqual(len(family), 7711) founders, non_founders, dangling, couples, children = ped.analyze(family) splits = ped.split_disjoint(family, children) self.assertEqual(sum(map(len, splits)), len(family)) self.assertEqual(set(family), set().union(*map(set, splits)))
def test_split_disjoint(self):
family, genotyped = read_ped_file(
os.path.join(DATA_DIR, 'ped_soup.ped'))
self.assertEqual(len(family), 7711)
founders, non_founders, dangling, couples, children = ped.analyze(
family)
splits = ped.split_disjoint(family, children)
self.assertEqual(sum(map(len, splits)), len(family))
self.assertEqual(set(family), set().union(*map(set, splits)))
def get_all_families(kb):
inds = kb.get_objects(kb.Individual)
not_one_parent = [i for i in inds if not
(((i.mother is None) or (i.father is None)) and
not (i.mother is None and i.father is None))
]
founders, non_founders, dangling, couples, children = ped.analyze(
not_one_parent
)
return ped.split_disjoint(not_one_parent, children)
def test_split_family(self):
family, genotyped = read_ped_file(os.path.join(DATA_DIR, 'ped_soup.ped'))
self.assertEqual(len(family), 7711)
founders, non_founders, dangling, couples, children = ped.analyze(family)
splits = ped.split_disjoint(family, children)
fams = []
max_complexity = ped.MAX_COMPLEXITY
for f in splits:
cbn = ped.compute_bit_complexity(f, genotyped)
if cbn > max_complexity:
subfs = ped.split_family(f, genotyped, max_complexity)
subfs_i = set().union(*map(set, subfs))
self.assertTrue(len(f) >= len(subfs_i))
self.assertTrue(len(set(f) - subfs_i) >= 0)
for s in subfs:
self.assertTrue(
ped.compute_bit_complexity(s, genotyped) <= max_complexity
)
def test_split_family(self):
family, genotyped = read_ped_file(
os.path.join(DATA_DIR, 'ped_soup.ped'))
self.assertEqual(len(family), 7711)
founders, non_founders, dangling, couples, children = ped.analyze(
family)
splits = ped.split_disjoint(family, children)
fams = []
max_complexity = ped.MAX_COMPLEXITY
for f in splits:
cbn = ped.compute_bit_complexity(f, genotyped)
if cbn > max_complexity:
subfs = ped.split_family(f, genotyped, max_complexity)
subfs_i = set().union(*map(set, subfs))
self.assertTrue(len(f) >= len(subfs_i))
self.assertTrue(len(set(f) - subfs_i) >= 0)
for s in subfs:
self.assertTrue(
ped.compute_bit_complexity(s, genotyped) <=
max_complexity)
