def test_surrogate_parents(self):
'''Find all surrogate parents of a node.'''
p = itu.Templates.problem_hut().pedigree
g = p.graph
assert_equal(pt.surrogate_parents(g, 1298, 0), {}, 'Unexpected surrogate parent set')
assert_equal(pt.surrogate_parents(g, 1298, 1), OrderedDict([(1480, 1), (1719, 1), (1217, 1), (1412, 1), (1413, 1)]), 'Unexpected surrogate parent set')
assert_equal(pt.surrogate_parents(g, 1298, 2), OrderedDict([(1480, 1), (1719, 1), (2028, 2), (1829, 2), (2064, 2), (2082, 2), (1217, 1), (1412, 1), (1413, 1), (2627, 2), (2628, 2), (2629, 2), (2630, 2), (2755, 2), (2756, 2), (1756, 2)]), 'Unexpected surrogate parent set')
assert_equal(pt.surrogate_parents(g, 1298, 3), OrderedDict([(1480, 1), (1719, 1), (2028, 2), (1829, 2), (2064, 2), (2082, 2), (2180, 3), (2158, 3), (2155, 3), (2070, 3), (2275, 3), (2278, 3), (2202, 3), (2171, 3), (1217, 1), (1412, 1), (1413, 1), (3236, 3), (2627, 2), (2628, 2), (2629, 2), (2630, 2), (617, 3), (1188, 3), (2755, 2), (1110, 3), (2756, 2), (1756, 2), (2982, 3), (1482, 3), (1484, 3), (1486, 3), (1487, 3), (1491, 3), (1492, 3), (2644, 3), (1728, 3), (134, 3), (1735, 3), (2635, 3), (2770, 3), (1749, 3), (1751, 3), (1752, 3), (1721, 3), (1754, 3), (1724, 3), (1726, 3)]), 'Unexpected surrogate parent set')
assert_equal(pt.surrogate_parents(g, 1298, 3, min_depth=2), OrderedDict([(2028, 2), (1829, 2), (2064, 2), (2082, 2), (2180, 3), (2158, 3), (2155, 3), (2070, 3), (2275, 3), (2278, 3), (2202, 3), (2171, 3), (3236, 3), (2627, 2), (2628, 2), (2629, 2), (2630, 2), (617, 3), (1188, 3), (2755, 2), (1110, 3), (2756, 2), (1756, 2), (2982, 3), (1482, 3), (1484, 3), (1486, 3), (1487, 3), (1491, 3), (1492, 3), (2644, 3), (1728, 3), (134, 3), (1735, 3), (2635, 3), (2770, 3), (1749, 3), (1751, 3), (1752, 3), (1721, 3), (1754, 3), (1724, 3), (1726, 3)]), 'Unexpected surrogate parent set')
def test_surrogate_parents(self):
'''Find all surrogate parents of a node.'''
p = itu.Templates.problem_hut().pedigree
g = p.graph
assert_equal(pt.surrogate_parents(g, 1298, 0), {},
'Unexpected surrogate parent set')
assert_equal(
pt.surrogate_parents(g, 1298, 1),
OrderedDict([(1480, 1), (1719, 1), (1217, 1), (1412, 1),
(1413, 1)]), 'Unexpected surrogate parent set')
assert_equal(
pt.surrogate_parents(g, 1298, 2),
OrderedDict([(1480, 1), (1719, 1), (2028, 2), (1829, 2), (2064, 2),
(2082, 2), (1217, 1), (1412, 1), (1413, 1), (2627, 2),
(2628, 2), (2629, 2), (2630, 2), (2755, 2), (2756, 2),
(1756, 2)]), 'Unexpected surrogate parent set')
assert_equal(
pt.surrogate_parents(g, 1298, 3),
OrderedDict([(1480, 1), (1719, 1), (2028, 2), (1829, 2), (2064, 2),
(2082, 2), (2180, 3), (2158, 3), (2155, 3), (2070, 3),
(2275, 3), (2278, 3), (2202, 3), (2171, 3), (1217, 1),
(1412, 1), (1413, 1), (3236, 3), (2627, 2), (2628, 2),
(2629, 2), (2630, 2), (617, 3), (1188, 3), (2755, 2),
(1110, 3), (2756, 2), (1756, 2), (2982, 3), (1482, 3),
(1484, 3), (1486, 3), (1487, 3), (1491, 3), (1492, 3),
(2644, 3), (1728, 3), (134, 3), (1735, 3), (2635, 3),
(2770, 3), (1749, 3), (1751, 3), (1752, 3), (1721, 3),
(1754, 3), (1724, 3), (1726, 3)]),
'Unexpected surrogate parent set')
assert_equal(
pt.surrogate_parents(g, 1298, 3, min_depth=2),
OrderedDict([(2028, 2), (1829, 2), (2064, 2), (2082, 2), (2180, 3),
(2158, 3), (2155, 3), (2070, 3), (2275, 3), (2278, 3),
(2202, 3), (2171, 3), (3236, 3), (2627, 2), (2628, 2),
(2629, 2), (2630, 2), (617, 3), (1188, 3), (2755, 2),
(1110, 3), (2756, 2), (1756, 2), (2982, 3), (1482, 3),
(1484, 3), (1486, 3), (1487, 3), (1491, 3), (1492, 3),
(2644, 3), (1728, 3), (134, 3), (1735, 3), (2635, 3),
(2770, 3), (1749, 3), (1751, 3), (1752, 3), (1721, 3),
(1754, 3), (1724, 3), (1726, 3)]),
'Unexpected surrogate parent set')
def in_neighborhood(sample, problem, min_path_length, max_path_length, fill_threshold):
'''Create a RelativeCollection with genotype relatives filled to fill_threshold of
at most d=max_path_length proximity.'''
genotyped_relatives = dict((x, y) for (x, y) in
surrogate_parents(problem.pedigree.graph, sample,
min_depth=min_path_length,
max_depth=max_path_length).iteritems()
if problem.is_genotyped(x))
f = problem.fill_fraction(sample=genotyped_relatives.keys())
r = RelativeCollection(sample)
if f.size:
filled = dict(zip(f[:, 0].astype('int'), f[:, 1]))
r += [(x, y) for (x, y) in genotyped_relatives.iteritems()
if filled[x] >= fill_threshold]
# Sort by ascending priority (increasing depth, then decreasing fill %)
# return a[np.lexsort((a[:, 1], -a[:, 2]))] if a.size else None
return r
def in_neighborhood(sample, problem, min_path_length, max_path_length,
fill_threshold):
'''Create a RelativeCollection with genotype relatives filled to fill_threshold of
at most d=max_path_length proximity.'''
genotyped_relatives = dict((x, y) for (
x, y) in surrogate_parents(problem.pedigree.graph,
sample,
min_depth=min_path_length,
max_depth=max_path_length).iteritems()
if problem.is_genotyped(x))
f = problem.fill_fraction(sample=genotyped_relatives.keys())
r = RelativeCollection(sample)
if f.size:
filled = dict(zip(f[:, 0].astype('int'), f[:, 1]))
r += [(x, y) for (x, y) in genotyped_relatives.iteritems()
if filled[x] >= fill_threshold]
# Sort by ascending priority (increasing depth, then decreasing fill %)
# return a[np.lexsort((a[:, 1], -a[:, 2]))] if a.size else None
return r
