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)
def test_compute_bit_complexity(self):
for cb, fname in manifest_reader():
family, genotyped = read_ped_file(os.path.join(DATA_DIR, fname))
cbn = ped.compute_bit_complexity(family, genotyped)
self.assertEqual(cb, cbn)
def test_compute_bit_complexity(self):
for cb, fname in manifest_reader():
family, genotyped = read_ped_file(os.path.join(DATA_DIR, fname))
cbn = ped.compute_bit_complexity(family, genotyped)
self.assertEqual(cb, cbn)