def test_ibd_segments_in_family(self):
'''Test locating recombination locations and subsequently IBD regions between
parent and child haplotypes.'''
segment_set = ibd.concatenate_segments(
ip.ibd_segments_in_family(self.haplotype, self.family,
PhaseParam.HET_FILL_THRESHOLD))
assert_segments_almost_equal(segment_set, [
((3, 172), (17080378, 18541497, 1.461, 0), ((1, 1), (2, 1))),
((193, 3218), (18996226, 51156934, 32.161, 1), ((1, 0), (2, 1))),
((0, 3218), (16484792, 51156934, 34.672, 4), ((1, 0), (3, 1))),
((3, 240), (17080378, 19593301, 2.513, 0), ((1, 0), (4, 1))),
((256, 3218), (19873357, 51156934, 31.284, 0), ((4, 1), (1, 1))),
((0, 3218), (16484792, 51156934, 34.672, 0), ((5, 1), (1, 0))),
((3, 2696), (17080378, 46630634, 29.550, 0), ((6, 1), (1, 1))),
((2718, 3218), (46853292, 51156934, 4.304, 1), ((1, 0), (6, 1))),
((0, 3218), (16484792, 51156934, 34.672, 0), ((1, 0), (7, 1))),
((3, 1908), (17080378, 36572515, 19.492, 0), ((8, 1), (1, 0))),
((1939, 3218), (36804282, 51156934, 14.353, 0), ((8, 1), (1, 1)))
],
full_data=True,
decimal=3,
err_msg='Wrong IBD segments')
assert_equal(segment_set.errors, [[
2997, 2997, 132, 1364, 2493, 2800, 132, 1364, 2493, 2800, 2997,
2997
], [1, 2, 1, 1, 1, 1, 3, 3, 3, 3, 1, 6]], 'Wrong genotype errors')
def test_ibd_segments_both_parents(self):
'''Test computing GERMLINE IBD segments.'''
h_mat = ig._HapMatrix(self.problem, self.sibs)
m = self.ibd_computer.ibd_segments(h_mat)
assert_segments_almost_equal(m,
[((0 , 344), (16484792, 21449028, 4.964, 0), ((2, 0), (4, 0))),
((0 , 344), (16484792, 21449028, 4.964, 0), ((1, 0), (4, 0))),
((0 , 780), (16484792, 26920270, 10.435, 0), ((4, 1), (2, 1))),
((2145, 2996), (39608193, 48759228, 9.151, 0), ((1, 1), (2, 1))),
((2145, 2996), (39608193, 48759228, 9.151, 0), ((4, 1), (2, 1))),
((885 , 3218), (27425790, 51156933, 23.731, 0), ((4, 1), (1, 1))),
((0 , 3218), (16484792, 51156933, 34.672, 0), ((2, 0), (1, 0)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments, raw')
# A transitive-logic test test to see that we don't miss any intervals with GERMLINE
m.group_to_disjoint(False)
assert_segments_almost_equal(m,
[((0 , 344), (16484792, 21449028, 4.964, 0), ((2, 0), (1, 0), (4, 0))),
((0 , 344), (16484792, 21449028, 4.964, 0), ((4, 1), (2, 1))),
((344 , 780), (21449028, 26920270, 5.471, 0), ((2, 0), (1, 0))),
((344 , 780), (21449028, 26920270, 5.471, 0), ((4, 1), (2, 1))),
((780 , 885), (26920270, 27425790, 0.506, 0), ((2, 0), (1, 0))),
((885 , 2145), (27425790, 39608193, 12.182, 0), ((2, 0), (1, 0))),
((885 , 2145), (27425790, 39608193, 12.182, 0), ((4, 1), (1, 1))),
((2145, 2996), (39608193, 48759228, 9.151, 0), ((4, 1), (1, 1), (2, 1))),
((2145, 2996), (39608193, 48759228, 9.151, 0), ((2, 0), (1, 0))),
((2996, 3218), (48759228, 51156933, 2.398, 0), ((2, 0), (1, 0))),
((2996, 3218), (48759228, 51156933, 2.398, 0), ((4, 1), (1, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments, grouped')
stats = np.array([(len(s.samples), s.length) for s in m])
best_segment = np.lexsort((-stats[:, 1], -stats[:, 0]))[0]
assert_equal(best_segment, 7, 'Wrong best segment (IBD set size + length)')
assert_almost_equal(m[best_segment].length, 9.15, decimal=2, err_msg='Wrong best segment (IBD set size + length)')
assert_equal(m[best_segment].samples, set([(4, 1), (1, 1), (2, 1)]), err_msg='Wrong best segment (IBD set size + length)')
def test_ibs_segments(self):
'''Test locating IBD segments between parent and child haplotypes.'''
(parent, child, hap1, hap2) = (1, 2, 0, 1)
het_snps = gt.where_heterozygous(self.haplotype.data, parent)
segment_set = ibd.ibs_segments(self.haplotype, parent, child, hap1,
hap2, het_snps, True)
assert_segments_almost_equal(
segment_set,
[((3, 172), (17080378, 18541497, 1.461, 0), ((1, 1), (2, 1))),
((193, 3218), (18996226, 51156934, 32.161, 1), ((1, 0), (2, 1)))],
full_data=True,
decimal=3,
err_msg='Wrong IBD segments')
segment_set = ibd.ibs_segments(self.haplotype,
parent,
child,
hap1,
hap2,
het_snps,
True,
length_bound='base_pair',
min_segment_length=10.0)
assert_segments_almost_equal(segment_set,
[((193, 3218),
(18996226, 51156934, 32.161, 1),
((1, 0), (2, 1)))],
full_data=True,
decimal=3,
err_msg='Wrong IBD segments')
def test_ibd_segments(self):
'''Test calculating IBD segments from child recombinations.'''
parent_type = PATERNAL
template = 2
(_, _, info) = self.child_recombinations(parent_type, template, remove_errors=True)
self.comparator.phase_parent_by_template(info)
#ibd.phase_by_ibd(self.problem, info.ibs_segments())
segment_set = ibd.concatenate_segments(x for x in info.ibs_segments())
#print segment_set.pprint_segments(True)
assert_segments_almost_equal(segment_set,
[((0 , 2800), (-1 , -1 , -1.000, 0), ((2, 0), (0, 0))),
((2800, 3218), (-1 , -1 , -1.000, 0), ((0, 1), (2, 0))),
((0 , 3218), (-1 , -1 , -1.000, 0), ((3, 0), (0, 0))),
((0 , 3218), (-1 , -1 , -1.000, 0), ((0, 0), (4, 0))),
((0 , 3218), (-1 , -1 , -1.000, 0), ((0, 1), (5, 0))),
((0 , 3218), (-1 , -1 , -1.000, 0), ((0, 0), (6, 0))),
((0 , 55), (-1 , -1 , -1.000, 0), ((0, 0), (7, 0))),
((55 , 2981), (-1 , -1 , -1.000, 0), ((0, 1), (7, 0))),
((2981, 3218), (-1 , -1 , -1.000, 0), ((0, 0), (7, 0))),
((0 , 637), (-1 , -1 , -1.000, 0), ((8, 0), (0, 0))),
((637 , 2447), (-1 , -1 , -1.000, 0), ((0, 1), (8, 0))),
((2447, 3218), (-1 , -1 , -1.000, 0), ((8, 0), (0, 0))),
((0 , 3218), (-1 , -1 , -1.000, 0), ((9, 0), (0, 0))),
((0 , 3218), (-1 , -1 , -1.000, 0), ((10, 0), (0, 0))),
((0 , 3046), (-1 , -1 , -1.000, 0), ((11, 0), (0, 0))),
((3046, 3218), (-1 , -1 , -1.000, 0), ((0, 1), (11, 0))),
((0 , 3081), (-1 , -1 , -1.000, 0), ((0, 1), (12, 0))),
((3081, 3218), (-1 , -1 , -1.000, 0), ((0, 0), (12, 0))),
((0 , 199), (-1 , -1 , -1.000, 0), ((0, 0), (13, 0))),
((199 , 3089), (-1 , -1 , -1.000, 0), ((0, 1), (13, 0))),
((3089, 3218), (-1 , -1 , -1.000, 0), ((0, 0), (13, 0))),
((0 , 860), (-1 , -1 , -1.000, 0), ((0, 0), (14, 0))),
((860 , 3218), (-1 , -1 , -1.000, 0), ((0, 1), (14, 0)))],
decimal=3, err_msg='Wrong IBD segments')
def test_ibs_segments(self):
'''Test computing GERMLINE IBD segments.'''
m = ig.ibd_germline(self.problem, self.sibs)
assert_equal(m.length, 24, 'Wrong # IBD grouped segments')
assert_segments_almost_equal(m,
[((1 , 434), (17065079, 23614026, 6.549, 0), ((0, 1), (3, 1), (4, 1), (1, 1))),
((1 , 434), (17065079, 23614026, 6.549, 0), ((5, 1), (0, 0), (4, 0))),
((1 , 434), (17065079, 23614026, 6.549, 0), ((3, 0), (1, 0))),
((434 , 537), (23614026, 24732045, 1.118, 0), ((0, 1), (3, 1), (4, 1))),
((434 , 537), (23614026, 24732045, 1.118, 0), ((5, 1), (0, 0), (4, 0))),
((537 , 848), (24732045, 27321172, 2.589, 0), ((3, 0), (5, 1), (0, 0), (4, 0))),
((537 , 848), (24732045, 27321172, 2.589, 0), ((0, 1), (3, 1), (4, 1))),
((537 , 848), (24732045, 27321172, 2.589, 0), ((1, 1), (5, 0))),
((848 , 948), (27321172, 27671082, 0.350, 0), ((0, 1), (3, 1), (4, 1))),
((848 , 948), (27321172, 27671082, 0.350, 0), ((3, 0), (5, 1), (0, 0))),
((848 , 948), (27321172, 27671082, 0.350, 0), ((1, 1), (5, 0))),
((948 , 2481), (27671082, 44544028, 16.873, 0), ((0, 1), (3, 1), (4, 1))),
((948 , 2481), (27671082, 44544028, 16.873, 0), ((3, 0), (5, 1), (0, 0))),
((948 , 2481), (27671082, 44544028, 16.873, 0), ((1, 1), (5, 0))),
((948 , 2481), (27671082, 44544028, 16.873, 0), ((1, 0), (4, 0))),
((2481, 2583), (44544028, 45330235, 0.786, 0), ((0, 1), (3, 1), (4, 1))),
((2481, 2583), (44544028, 45330235, 0.786, 0), ((3, 0), (5, 1), (0, 0))),
((2481, 2583), (44544028, 45330235, 0.786, 0), ((1, 0), (4, 0))),
((2583, 3107), (45330235, 49669743, 4.340, 0), ((0, 1), (3, 1), (4, 1), (5, 0))),
((2583, 3107), (45330235, 49669743, 4.340, 0), ((3, 0), (5, 1), (0, 0))),
((2583, 3107), (45330235, 49669743, 4.340, 0), ((1, 0), (4, 0))),
((3107, 3218), (49669743, 51156933, 1.487, 0), ((0, 1), (3, 1), (4, 1), (1, 1), (5, 0))),
((3107, 3218), (49669743, 51156933, 1.487, 0), ((3, 0), (5, 1), (0, 0))),
((3107, 3218), (49669743, 51156933, 1.487, 0), ((1, 0), (4, 0)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
stats = np.array([(len(s.samples), s.length) for s in m])
best_segment = np.lexsort((-stats[:, 1], -stats[:, 0]))[0]
assert_equal(best_segment, 21, 'Wrong best segment (IBD set size + length)')
def test_ibd_segments_parent_child(self):
'''Test IBD segments that are apparently cut too short between a parent and child.'''
parent = self.family.mother
child = 2
parent_type = MATERNAL
h = self.problem.haplotype
het_snps = gt.where_heterozygous(h.data, parent)
segment_set = ip.ibd_segments_parent_child(h, parent, child, parent_type, het_snps)
assert_segments_almost_equal(segment_set,
[((2 , 2650), (17075353, 45892433, 28.817, 0), ((1, 1), (2, 1))),
((2657, 3218), (45940934, 51156934, 5.216, 2), ((1, 0), (2, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
def test_ibd_segments(self):
'''Test computing GERMLINE IBD segments.'''
m = self.ibd_computer.ibd_segments(ig._HapMatrix(self.problem, self.sibs)).group_to_disjoint()
assert_segments_almost_equal(m,
[((0 , 20), (16484792, 17318333, 0.834, 0), ((3, 1), (4, 1), (1, 1), (2, 1))),
((0 , 20), (16484792, 17318333, 0.834, 0), ((0, 1), (3, 0), (5, 0))),
((0 , 20), (16484792, 17318333, 0.834, 0), ((2, 0), (0, 0), (4, 0))),
((0 , 20), (16484792, 17318333, 0.834, 0), ((5, 1), (1, 0))),
((20 , 121), (17318333, 18235305, 0.917, 0), ((5, 1), (4, 1), (1, 1), (2, 1))),
((20 , 121), (17318333, 18235305, 0.917, 0), ((0, 1), (3, 0), (5, 0))),
((20 , 121), (17318333, 18235305, 0.917, 0), ((2, 0), (0, 0), (4, 0))),
((121 , 224), (18235305, 19455836, 1.221, 0), ((5, 1), (4, 1), (1, 1), (2, 1))),
((121 , 224), (18235305, 19455836, 1.221, 0), ((0, 1), (3, 0), (5, 0))),
((121 , 224), (18235305, 19455836, 1.221, 0), ((0, 0), (4, 0))),
((121 , 224), (18235305, 19455836, 1.221, 0), ((1, 0), (3, 1))),
((224 , 828), (19455836, 27236071, 7.780, 0), ((0, 1), (3, 0), (5, 0), (2, 0))),
((224 , 828), (19455836, 27236071, 7.780, 0), ((5, 1), (4, 1), (1, 1), (2, 1))),
((224 , 828), (19455836, 27236071, 7.780, 0), ((0, 0), (4, 0))),
((224 , 828), (19455836, 27236071, 7.780, 0), ((1, 0), (3, 1))),
((828 , 2039), (27236071, 37707962, 10.472, 0), ((0, 1), (3, 0), (5, 0), (2, 0))),
((828 , 2039), (27236071, 37707962, 10.472, 0), ((1, 0), (3, 1), (4, 1))),
((828 , 2039), (27236071, 37707962, 10.472, 0), ((5, 1), (1, 1), (2, 1))),
((828 , 2039), (27236071, 37707962, 10.472, 0), ((0, 0), (4, 0))),
((2039, 2442), (37707962, 44264502, 6.557, 0), ((0, 1), (3, 0), (5, 0), (2, 0))),
((2039, 2442), (37707962, 44264502, 6.557, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2039, 2442), (37707962, 44264502, 6.557, 0), ((0, 0), (4, 0))),
((2039, 2442), (37707962, 44264502, 6.557, 0), ((1, 0), (4, 1))),
((2442, 2542), (44264502, 44930087, 0.666, 0), ((0, 1), (3, 0), (5, 0), (2, 0))),
((2442, 2542), (44264502, 44930087, 0.666, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2442, 2542), (44264502, 44930087, 0.666, 0), ((1, 0), (4, 1))),
((2542, 2642), (44930087, 45823327, 0.893, 0), ((0, 1), (3, 0), (4, 0), (5, 0), (2, 0))),
((2542, 2642), (44930087, 45823327, 0.893, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2542, 2642), (44930087, 45823327, 0.893, 0), ((1, 0), (4, 1))),
((2642, 2742), (45823327, 47169675, 1.346, 0), ((0, 1), (3, 0), (5, 0), (4, 0))),
((2642, 2742), (45823327, 47169675, 1.346, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2642, 2742), (45823327, 47169675, 1.346, 0), ((1, 0), (4, 1))),
((2742, 2942), (47169675, 48530211, 1.361, 0), ((0, 1), (3, 0), (5, 0), (4, 0))),
((2742, 2942), (47169675, 48530211, 1.361, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2742, 2942), (47169675, 48530211, 1.361, 0), ((2, 0), (0, 0))),
((2742, 2942), (47169675, 48530211, 1.361, 0), ((1, 0), (4, 1))),
((2942, 3042), (48530211, 49168613, 0.638, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2942, 3042), (48530211, 49168613, 0.638, 0), ((0, 1), (3, 0), (4, 0))),
((2942, 3042), (48530211, 49168613, 0.638, 0), ((2, 0), (0, 0))),
((2942, 3042), (48530211, 49168613, 0.638, 0), ((1, 0), (4, 1))),
((3042, 3218), (49168613, 51156933, 1.988, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((3042, 3218), (49168613, 51156933, 1.988, 0), ((0, 1), (3, 0), (4, 0))),
((3042, 3218), (49168613, 51156933, 1.988, 0), ((2, 0), (0, 0), (5, 0))),
((3042, 3218), (49168613, 51156933, 1.988, 0), ((1, 0), (4, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments, grouped')
stats = np.array([(len(s.samples), s.length) for s in m])
best_segment = np.lexsort((-stats[:, 1], -stats[:, 0]))[0]
assert_equal(best_segment, 26, 'Wrong best segment (IBD set size + length)')
def test_ibd_segments_ibdld(self):
'''Calculate IBD segments in a nuclear family using IBDLD.'''
segment_cache = im.ibdld.ibd_ld.IbdSegmentGlobalCacheIbdld(itu.FAMILY7 + '.ibd')
segment_computer = im.ibdld.ibd_ld.IbdSegmentComputerIbdld(segment_cache, self.haplotype,
chrom=22,
sample_id=self.problem.pedigree.sample_id,
samples=[2, 8],
threshold=0.9,
params=PhaseParam())
segment_set = segment.break_and_group_segments(segment_computer.segments)
assert_segments_almost_equal(segment_set,
[((38 , 2849), [], ((8, 1), (2, 1)))],
full_data=False, decimal=3, err_msg='Wrong grouped IBDLD IBD segments')
assert_equal(segment_set.errors, empty_errors_array(), 'IBDLD does not support errors but they are output?!')
def test_ibd_segments_both_parents(self):
'''Test computing GERMLINE IBD segments.'''
h_mat = ig._HapMatrix(self.problem, self.sibs)
m = self.ibd_computer.ibd_segments(h_mat)
assert_segments_almost_equal(
m,
[((0, 344), (16484792, 21449028, 4.964, 0), ((2, 0), (4, 0))),
((0, 344), (16484792, 21449028, 4.964, 0), ((1, 0), (4, 0))),
((0, 780), (16484792, 26920270, 10.435, 0), ((4, 1), (2, 1))),
((2145, 2996), (39608193, 48759228, 9.151, 0), ((1, 1), (2, 1))),
((2145, 2996), (39608193, 48759228, 9.151, 0), ((4, 1), (2, 1))),
((885, 3218), (27425790, 51156933, 23.731, 0), ((4, 1), (1, 1))),
((0, 3218), (16484792, 51156933, 34.672, 0), ((2, 0), (1, 0)))],
full_data=True,
decimal=3,
err_msg='Wrong IBD segments, raw')
# A transitive-logic test test to see that we don't miss any intervals with GERMLINE
m.group_to_disjoint(False)
assert_segments_almost_equal(
m,
[((0, 344), (16484792, 21449028, 4.964, 0), ((2, 0), (1, 0),
(4, 0))),
((0, 344), (16484792, 21449028, 4.964, 0), ((4, 1), (2, 1))),
((344, 780), (21449028, 26920270, 5.471, 0), ((2, 0), (1, 0))),
((344, 780), (21449028, 26920270, 5.471, 0), ((4, 1), (2, 1))),
((780, 885), (26920270, 27425790, 0.506, 0), ((2, 0), (1, 0))),
((885, 2145), (27425790, 39608193, 12.182, 0), ((2, 0), (1, 0))),
((885, 2145), (27425790, 39608193, 12.182, 0), ((4, 1), (1, 1))),
((2145, 2996), (39608193, 48759228, 9.151, 0), ((4, 1), (1, 1),
(2, 1))),
((2145, 2996), (39608193, 48759228, 9.151, 0), ((2, 0), (1, 0))),
((2996, 3218), (48759228, 51156933, 2.398, 0), ((2, 0), (1, 0))),
((2996, 3218), (48759228, 51156933, 2.398, 0), ((4, 1), (1, 1)))],
full_data=True,
decimal=3,
err_msg='Wrong IBD segments, grouped')
stats = np.array([(len(s.samples), s.length) for s in m])
best_segment = np.lexsort((-stats[:, 1], -stats[:, 0]))[0]
assert_equal(best_segment, 7,
'Wrong best segment (IBD set size + length)')
assert_almost_equal(
m[best_segment].length,
9.15,
decimal=2,
err_msg='Wrong best segment (IBD set size + length)')
assert_equal(m[best_segment].samples,
set([(4, 1), (1, 1), (2, 1)]),
err_msg='Wrong best segment (IBD set size + length)')
def test_ibs_segments(self):
'''Test locating IBD segments between parent and child haplotypes.'''
(parent, child, hap1, hap2) = (1, 2, 0, 1)
het_snps = gt.where_heterozygous(self.haplotype.data, parent)
segment_set = ibd.ibs_segments(self.haplotype, parent, child, hap1, hap2, het_snps, True)
assert_segments_almost_equal(segment_set,
[((3 , 172), (17080378, 18541497, 1.461, 0), ((1, 1), (2, 1))),
((193 , 3218), (18996226, 51156934, 32.161, 1), ((1, 0), (2, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
segment_set = ibd.ibs_segments(self.haplotype, parent, child, hap1, hap2, het_snps, True,
length_bound='base_pair', min_segment_length=10.0)
assert_segments_almost_equal(segment_set,
[((193 , 3218), (18996226, 51156934, 32.161, 1), ((1, 0), (2, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
def test_ibd_segments_ibs(self):
'''Test locating IBD segments between distant individuals. No IBD posterior filter (IBS=>IBD).'''
relatives = self.__phased_sibs(self.s)
segment_set = im.idist.ibd_segments_with_relatives(self.problem, self.s, relatives, self.params,
im.ibd_distant.prob_ibd_ibs)
segment_set.group_to_disjoint()
assert_segments_almost_equal(segment_set,
[((0 , 38 ), (16484792, 17561913, 1.077, 0), ((5, 1),(1, 0),(1, 1),(2, 1))),
((38 , 180 ), (17561913, 18562888, 1.001, 0), ((1, 0),(1, 1),(2, 1))),
((180 , 195 ), (18562888, 19030336, 0.467, 0), ((1, 0),(1, 1),(5, 0),(2, 1))),
((195 , 329 ), (19030336, 21242544, 2.212, 0), ((1, 0),(5, 0),(2, 1))),
((329 , 369 ), (21242544, 22485301, 1.243, 0), ((5, 1),(1, 0),(5, 0),(2, 1))),
((369 , 435 ), (22485301, 23627369, 1.142, 0), ((1, 0),(5, 0),(2, 1))),
((435 , 506 ), (23627369, 24235198, 0.608, 0), ((1, 0),(1, 1),(5, 0),(2, 1))),
((506 , 581 ), (24235198, 25304473, 1.069, 0), ((5, 1),(1, 0),(1, 1),(5, 0),(2, 1))),
((581 , 865 ), (25304473, 27370273, 2.066, 0), ((1, 0),(1, 1),(5, 0),(2, 1))),
((865 , 1032), (27370273, 28120707, 0.750, 0), ((1, 0),(2, 1),(1, 1),(5, 0),(4, 0))),
((1032, 1037), (28120707, 28165334, 0.045, 0), ((5, 0),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((1037, 1109), (28165334, 29400515, 1.235, 0), ((5, 0),(5, 1),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((1109, 1138), (29400515, 29495373, 0.095, 0), ((1, 0),(2, 1),(1, 1),(5, 0),(4, 0))),
((1138, 1249), (29495373, 30864692, 1.369, 0), ((5, 0),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((1249, 1276), (30864692, 31207207, 0.343, 0), ((1, 0),(2, 1),(1, 1),(5, 0),(4, 0))),
((1276, 1460), (31207207, 33291742, 2.085, 0), ((5, 0),(5, 1),(1, 0),(1, 1),(2, 1),(4, 0))),
((1460, 1792), (33291742, 35344317, 2.053, 0), ((1, 0),(2, 1),(1, 1),(5, 0),(4, 0))),
((1792, 1934), (35344317, 36746079, 1.402, 0), ((5, 0),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((1934, 2008), (36746079, 37383809, 0.638, 0), ((1, 0),(2, 1),(1, 1),(5, 0),(4, 0))),
((2008, 2052), (37383809, 37977282, 0.593, 0), ((5, 0),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2052, 2068), (37977282, 38538246, 0.561, 0), ((5, 0),(5, 1),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2068, 2170), (38538246, 39988277, 1.450, 0), ((5, 0),(5, 1),(1, 0),(1, 1),(2, 1),(4, 0))),
((2170, 2187), (39988277, 40351438, 0.363, 0), ((1, 0),(2, 1),(1, 1),(5, 0),(4, 0))),
((2187, 2189), (40351438, 40395084, 0.044, 0), ((5, 0),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2189, 2269), (40395084, 42235352, 1.840, 0), ((5, 0),(5, 1),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2269, 2313), (42235352, 42919125, 0.684, 0), ((5, 0),(5, 1),(1, 0),(1, 1),(2, 1),(4, 0))),
((2313, 2314), (42919125, 42982572, 0.063, 0), ((5, 0),(5, 1),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2314, 2315), (42982572, 43013836, 0.031, 0), ((5, 0),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2315, 2393), (43013836, 44023173, 1.009, 0), ((5, 0),(5, 1),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2393, 2414), (44023173, 44101411, 0.078, 0), ((5, 0),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2414, 2598), (44101411, 45409136, 1.308, 0), ((1, 0),(2, 1),(1, 1),(5, 0),(4, 0))),
((2598, 2661), (45409136, 45972017, 0.563, 0), ((1, 0),(1, 1),(2, 1),(4, 0))),
((2661, 2666), (45972017, 46060541, 0.089, 0), ((5, 1),(1, 0),(1, 1),(2, 1),(4, 0))),
((2666, 2744), (46060541, 47175815, 1.115, 0), ((5, 0),(5, 1),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((2744, 2779), (47175815, 47387316, 0.212, 0), ((5, 0),(5, 1),(1, 0),(1, 1),(2, 1),(4, 0))),
((2779, 2835), (47387316, 47786315, 0.399, 0), ((1, 0),(2, 1),(1, 1),(5, 0),(4, 0))),
((2835, 3043), (47786315, 49171641, 1.385, 0), ((1, 0),(1, 1),(2, 1),(4, 0))),
((3043, 3178), (49171641, 50120525, 0.949, 0), ((5, 0),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0))),
((3178, 3218), (50120525, 51156934, 1.036, 0), ((5, 0),(5, 1),(1, 0),(4, 1),(1, 1),(2, 1),(4, 0)))],
decimal=3, err_msg='Wrong IBD segments')
def test_ibd_segments_in_family(self):
'''Test locating recombination locations and subsequently IBD regions between
parent and child haplotypes.'''
segment_set = ibd.concatenate_segments(ip.ibd_segments_in_family(self.haplotype, self.family,
PhaseParam.HET_FILL_THRESHOLD))
assert_segments_almost_equal(segment_set,
[((3 , 172), (17080378, 18541497, 1.461, 0), ((1, 1), (2, 1))),
((193 , 3218), (18996226, 51156934, 32.161, 1), ((1, 0), (2, 1))),
((0 , 3218), (16484792, 51156934, 34.672, 4), ((1, 0), (3, 1))),
((3 , 240), (17080378, 19593301, 2.513, 0), ((1, 0), (4, 1))),
((256 , 3218), (19873357, 51156934, 31.284, 0), ((4, 1), (1, 1))),
((0 , 3218), (16484792, 51156934, 34.672, 0), ((5, 1), (1, 0))),
((3 , 2696), (17080378, 46630634, 29.550, 0), ((6, 1), (1, 1))),
((2718, 3218), (46853292, 51156934, 4.304, 1), ((1, 0), (6, 1))),
((0 , 3218), (16484792, 51156934, 34.672, 0), ((1, 0), (7, 1))),
((3 , 1908), (17080378, 36572515, 19.492, 0), ((8, 1), (1, 0))),
((1939, 3218), (36804282, 51156934, 14.353, 0), ((8, 1), (1, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
assert_equal(segment_set.errors,
[[2997, 2997, 132, 1364, 2493, 2800, 132, 1364, 2493, 2800, 2997, 2997],
[ 1, 2, 1, 1, 1, 1, 3, 3, 3, 3, 1, 6]],
'Wrong genotype errors')
def test_ibd_segments(self):
'''Test computing GERMLINE IBD segments.'''
h_mat = ig._HapMatrix(self.problem, self.sibs)
m = self.ibd_computer.ibd_segments(h_mat)
m.group_to_disjoint()
assert_segments_almost_equal(m,
[((0 , 235), (16484792, 19567818, 3.083, 0), ((3, 0), (1, 0), (5, 0))),
((0 , 235), (16484792, 19567818, 3.083, 0), ((5, 1), (3, 1), (2, 1))),
((235 , 345), (19567818, 21809185, 2.241, 0), ((3, 0), (1, 0), (5, 0))),
((235 , 345), (19567818, 21809185, 2.241, 0), ((5, 1), (3, 1))),
((345 , 450), (21809185, 23817240, 2.008, 0), ((3, 0), (1, 0))),
((345 , 450), (21809185, 23817240, 2.008, 0), ((5, 1), (3, 1))),
((345 , 450), (21809185, 23817240, 2.008, 0), ((1, 1), (2, 1))),
((450 , 781), (23817240, 26924312, 3.107, 0), ((3, 0), (1, 0))),
((450 , 781), (23817240, 26924312, 3.107, 0), ((5, 1), (3, 1))),
((450 , 781), (23817240, 26924312, 3.107, 0), ((1, 1), (2, 1))),
((450 , 781), (23817240, 26924312, 3.107, 0), ((2, 0), (5, 0))),
((781 , 886), (26924312, 27427698, 0.503, 0), ((3, 0), (1, 0))),
((781 , 886), (26924312, 27427698, 0.503, 0), ((1, 1), (2, 1))),
((781 , 886), (26924312, 27427698, 0.503, 0), ((2, 0), (5, 0))),
((886 , 2157), (27427698, 39797178, 12.369, 0), ((5, 1), (1, 1), (2, 1))),
((886 , 2157), (27427698, 39797178, 12.369, 0), ((3, 0), (1, 0))),
((886 , 2157), (27427698, 39797178, 12.369, 0), ((2, 0), (5, 0))),
((2157, 2791), (39797178, 47440321, 7.643, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2157, 2791), (39797178, 47440321, 7.643, 0), ((3, 0), (1, 0))),
((2157, 2791), (39797178, 47440321, 7.643, 0), ((2, 0), (5, 0))),
((2791, 2901), (47440321, 48282594, 0.842, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2791, 2901), (47440321, 48282594, 0.842, 0), ((3, 0), (1, 0))),
((2901, 3012), (48282594, 48855412, 0.573, 0), ((5, 1), (3, 1), (1, 1), (2, 1))),
((2901, 3012), (48282594, 48855412, 0.573, 0), ((3, 0), (2, 0), (1, 0))),
((3012, 3218), (48855412, 51156933, 2.302, 0), ((3, 0), (2, 0), (1, 0))),
((3012, 3218), (48855412, 51156933, 2.302, 0), ((5, 1), (1, 1), (2, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
stats = np.array([(len(s.samples), s.length) for s in m])
best_segment = np.lexsort((-stats[:, 1], -stats[:, 0]))[0]
#print np.lexsort((-stats[:, 1], -stats[:, 0]))
# print m[best_segment]
assert_equal(best_segment, 17, 'Wrong best segment (IBD set size + length)')
def test_global_ibd_segments(self):
'''Debug error that appeared after stage 2 - child had wrong hap color at SNP 2960
in the middle of a long IBD segment. This error doesn''t appear in this isolated test.
It depends on the ordering of processing samples and segments.'''
# Before stage 2: no IBD segments should exist
problem = im.io.read_npz(im.itu.FAMILY4_STAGE1)
im.itu.assert_problem_stats(problem, 38616, 35586, 22)
ibd = problem.info.ibd
assert_equal(ibd.length, 0, 'Before stage 2: no IBD segments should exist')
assert_equal(problem.h[2955:2965, 1, 0], [2, 2, 2, 2, 2, 2, 2, 2, 2, 0], 'Wrong mother haplotype')
assert_equal(problem.h[2955:2965, 4, 1], [0, 0, 0, 0, 0, 0, 0, 0, 0, 1], 'Wrong child haplotype')
im.phase_family.family_phaser().run(problem, im.PhaseParam())
# After: check IBD segment; (1, 0), (4, 1) should be IBD around SNP 2960
assert_segments_almost_equal(ibd,
[((0 , 176), (16484792, 18545634, 2.061, 0), ((2, 0), (0, 0))),
((187 , 2687), (18895227, 46242359, 27.347, 1), ((0, 1), (2, 0))),
((2687, 3216), (46336181, 51103692, 4.768, 0), ((2, 0), (0, 0))),
((0 , 3218), (16484792, 51156933, 34.672, 0), ((0, 1), (3, 0))),
((0 , 2470), (16484792, 44456692, 27.972, 0), ((0, 0), (4, 0))),
((2473, 3216), (44515806, 51103692, 6.588, 1), ((0, 1), (4, 0))),
((0 , 2985), (16484792, 48709188, 32.224, 0), ((0, 1), (5, 0))),
((2993, 3216), (48742097, 51103692, 2.362, 0), ((0, 0), (5, 0))),
((0 , 3218), (16484792, 51156933, 34.672, 0), ((1, 1), (2, 1))),
((4 , 36), (17087656, 17434521, 0.347, 0), ((3, 1), (1, 1))),
((42 , 2035), (17587680, 37662436, 20.075, 1), ((1, 0), (3, 1))),
((2047, 3217), (37902926, 51140316, 13.237, 0), ((3, 1), (1, 1))),
((11 , 804), (17285049, 27091750, 9.807, 0), ((4, 1), (1, 1))),
((823 , 3217), (27200942, 51140316, 23.939, 0), ((1, 0), (4, 1))),
((11 , 14), (17285049, 17307742, 0.023, 0), ((5, 1), (1, 0))),
((31 , 3217), (17415572, 51140316, 33.725, 1), ((5, 1), (1, 1)))],
decimal=3, err_msg='Wrong IBD segments')
im.itu.assert_problem_stats(problem, 38616, 38576, 30)
assert_equal(problem.h[2955:2965, 1, 0], [2, 2, 2, 2, 2, 2, 2, 2, 2, 1], 'Wrong mother haplotype')
assert_equal(problem.h[2955:2965, 4, 1], [2, 2, 2, 2, 2, 2, 2, 2, 2, 1], 'Wrong child haplotype')
def test_ibd_segments_hmm(self):
'''Test locating IBD segments between the unphased proband and its sib surrogate parents.
Uses HMM IBD posterior.'''
relatives = self.__phased_sibs(self.s)
segment_set = im.idist.ibd_segments_with_relatives(self.problem, self.s, relatives, PhaseParam(debug=False),
im.ibd_hmm.prob_ibd_hmm)
segment_set.group_to_disjoint()
assert_segments_almost_equal(segment_set,
[((0 , 96 ), (16484792, 17948473, 1.464, 0), ((2, 0),(3, 1),(4, 1),(2, 1))),
((96 , 344 ), (17948473, 21460008, 3.512, 0), ((3, 1),(4, 1),(2, 1))),
((344 , 380 ), (21460008, 22554306, 1.094, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((380 , 383 ), (22554306, 22555078, 0.001, 0), ((3, 1),(4, 1),(2, 1))),
((383 , 438 ), (22555078, 23636541, 1.081, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((438 , 442 ), (23636541, 23695404, 0.059, 0), ((3, 1),(4, 1),(2, 1))),
((442 , 519 ), (23695404, 24406778, 0.711, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((519 , 557 ), (24406778, 25088629, 0.682, 0), ((0, 1),(2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((557 , 951 ), (25088629, 27698217, 2.610, 0), ((0, 1),(3, 1),(4, 1),(2, 1))),
((951 , 969 ), (27698217, 27832985, 0.135, 0), ((0, 1),(2, 0),(3, 1),(4, 1),(2, 1))),
((969 , 1019), (27832985, 28093392, 0.260, 0), ((2, 0),(3, 1),(4, 1),(2, 1))),
((1019, 1147), (28093392, 29670939, 1.578, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((1147, 1188), (29670939, 30113960, 0.443, 0), ((2, 0),(3, 1),(4, 1),(2, 1))),
((1188, 1403), (30113960, 32950053, 2.836, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((1403, 1943), (32950053, 36891858, 3.942, 0), ((2, 0),(3, 1),(4, 1),(2, 1))),
((1943, 2053), (36891858, 37982012, 1.090, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((2053, 2055), (37982012, 38086574, 0.105, 0), ((2, 0),(3, 1),(4, 1),(2, 1))),
((2055, 2133), (38086574, 39454432, 1.368, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((2133, 2174), (39454432, 40018212, 0.564, 0), ((2, 0),(3, 1),(4, 1),(2, 1))),
((2174, 2221), (40018212, 41107688, 1.089, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((2221, 2612), (41107688, 45515269, 4.408, 0), ((2, 0),(3, 1),(4, 1),(2, 1))),
((2612, 2661), (45515269, 45972017, 0.457, 0), ((2, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((2661, 2735), (45972017, 47094390, 1.122, 0), ((0, 1),(0, 0),(3, 1),(2, 1),(2, 0),(1, 0),(4, 1),(1, 1),(4, 0))),
((2735, 2945), (47094390, 48569604, 1.475, 0), ((2, 0),(0, 0),(1, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((2945, 2991), (48569604, 48741583, 0.172, 0), ((2, 0),(0, 0),(1, 0),(3, 1),(4, 1),(4, 0))),
((2991, 3127), (48741583, 49752332, 1.011, 0), ((2, 0),(0, 0),(1, 0),(3, 1),(4, 1),(2, 1),(4, 0))),
((3127, 3177), (49752332, 50120255, 0.368, 0), ((2, 0),(1, 0),(3, 1),(4, 1),(0, 0))),
((3177, 3218), (50120255, 51156934, 1.037, 0), ((0, 1),(0, 0),(3, 1),(2, 1),(2, 0),(1, 0),(4, 1),(1, 1),(4, 0)))],
decimal=3, err_msg='Wrong IBD segments')
def test_ibd_segments_in_family(self):
'''Test locating recombination locations and subsequently IBD regions between
parent and child haplotypes.'''
segment_set = ibd.concatenate_segments(ip.ibd_segments_in_family(self.problem.haplotype, self.family,
PhaseParam.HET_FILL_THRESHOLD))
assert_segments_almost_equal(segment_set,
[((4 , 1411), (17087656, 32978753, 15.891, 0), ((2, 0), (0, 0))),
((1413, 3215), (33013062, 51103692, 18.091, 1), ((0, 1), (2, 0))),
((0 , 3218), (16484792, 51156934, 34.672, 1), ((0, 1), (3, 0))),
((4 , 2551), (17087656, 45007348, 27.920, 1), ((0, 1), (4, 0))),
((2569, 3215), (45198494, 51103692, 5.905, 0), ((0, 0), (4, 0))),
((0 , 3218), (16484792, 51156934, 34.672, 1), ((0, 0), (5, 0))),
((4 , 795), (17087656, 27011420, 9.924, 0), ((0, 0), (6, 0))),
((805 , 3215), (27119061, 51103692, 23.985, 1), ((0, 1), (6, 0))),
((2 , 2650), (17075353, 45892433, 28.817, 0), ((1, 1), (2, 1))),
((2657, 3218), (45940934, 51156934, 5.216, 2), ((1, 0), (2, 1))),
((1 , 576), (17065079, 25228375, 8.163, 0), ((3, 1), (1, 1))),
((600 , 3218), (25444874, 51156934, 25.712, 2), ((1, 0), (3, 1))),
((2 , 1978), (17075353, 37228277, 20.153, 2), ((1, 0), (4, 1))),
((2019, 3218), (37509844, 51156934, 13.647, 0), ((4, 1), (1, 1))),
((0 , 3218), (16484792, 51156934, 34.672, 3), ((5, 1), (1, 0))),
((2 , 301), (17075353, 20993766, 3.918, 0), ((6, 1), (1, 1))),
((334 , 3218), (21363960, 51156934, 29.793, 2), ((1, 0), (6, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
# Check that there are at most 4 distinct haplotypes at each SNP
segment_set.group_to_disjoint(True)
assert_segments_almost_equal(segment_set,
[((0 , 1), (16484792, 17065079, 0.580, 0), ((5, 1), (1, 0))),
((0 , 1), (16484792, 17065079, 0.580, 0), ((0, 1), (3, 0))),
((0 , 1), (16484792, 17065079, 0.580, 0), ((0, 0), (5, 0))),
((1 , 2), (17065079, 17075353, 0.010, 0), ((5, 1), (1, 0))),
((1 , 2), (17065079, 17075353, 0.010, 0), ((3, 1), (1, 1))),
((1 , 2), (17065079, 17075353, 0.010, 0), ((0, 1), (3, 0))),
((1 , 2), (17065079, 17075353, 0.010, 0), ((0, 0), (5, 0))),
((2 , 4), (17075353, 17087656, 0.012, 0), ((0, 0), (5, 0))),
((2 , 4), (17075353, 17087656, 0.012, 0), ((0, 1), (3, 0))),
((2 , 4), (17075353, 17087656, 0.012, 0), ((6, 1), (3, 1), (1, 1), (2, 1))),
((2 , 4), (17075353, 17087656, 0.012, 0), ((5, 1), (1, 0), (4, 1))),
((4 , 301), (17087656, 20993766, 3.906, 0), ((2, 0), (0, 0), (6, 0), (5, 0))),
((4 , 301), (17087656, 20993766, 3.906, 0), ((0, 1), (3, 0), (4, 0))),
((4 , 301), (17087656, 20993766, 3.906, 0), ((6, 1), (3, 1), (1, 1), (2, 1))),
((4 , 301), (17087656, 20993766, 3.906, 0), ((5, 1), (1, 0), (4, 1))),
((301 , 334), (20993766, 21363960, 0.370, 0), ((2, 0), (0, 0), (6, 0), (5, 0))),
((301 , 334), (20993766, 21363960, 0.370, 0), ((0, 1), (3, 0), (4, 0))),
((301 , 334), (20993766, 21363960, 0.370, 0), ((3, 1), (1, 1), (2, 1))),
((301 , 334), (20993766, 21363960, 0.370, 0), ((5, 1), (1, 0), (4, 1))),
((334 , 576), (21363960, 25228375, 3.864, 0), ((2, 0), (0, 0), (6, 0), (5, 0))),
((334 , 576), (21363960, 25228375, 3.864, 0), ((0, 1), (3, 0), (4, 0))),
((334 , 576), (21363960, 25228375, 3.864, 0), ((3, 1), (1, 1), (2, 1))),
((334 , 576), (21363960, 25228375, 3.864, 0), ((5, 1), (6, 1), (4, 1), (1, 0))),
((576 , 600), (25228375, 25444874, 0.216, 0), ((1, 1), (2, 1))),
((576 , 600), (25228375, 25444874, 0.216, 0), ((2, 0), (0, 0), (6, 0), (5, 0))),
((576 , 600), (25228375, 25444874, 0.216, 0), ((0, 1), (3, 0), (4, 0))),
((576 , 600), (25228375, 25444874, 0.216, 0), ((5, 1), (6, 1), (4, 1), (1, 0))),
((600 , 795), (25444874, 27011420, 1.567, 0), ((5, 1), (6, 1), (3, 1), (4, 1), (1, 0))),
((600 , 795), (25444874, 27011420, 1.567, 0), ((2, 0), (0, 0), (6, 0), (5, 0))),
((600 , 795), (25444874, 27011420, 1.567, 0), ((0, 1), (3, 0), (4, 0))),
((600 , 795), (25444874, 27011420, 1.567, 0), ((1, 1), (2, 1))),
((795 , 805), (27011420, 27119061, 0.108, 0), ((5, 1), (6, 1), (3, 1), (4, 1), (1, 0))),
((795 , 805), (27011420, 27119061, 0.108, 0), ((2, 0), (0, 0), (5, 0))),
((795 , 805), (27011420, 27119061, 0.108, 0), ((0, 1), (3, 0), (4, 0))),
((795 , 805), (27011420, 27119061, 0.108, 0), ((1, 1), (2, 1))),
((805 , 1411), (27119061, 32978753, 5.860, 0), ((5, 1), (6, 1), (3, 1), (4, 1), (1, 0))),
((805 , 1411), (27119061, 32978753, 5.860, 0), ((2, 0), (0, 0), (5, 0))),
((805 , 1411), (27119061, 32978753, 5.860, 0), ((0, 1), (3, 0), (6, 0), (4, 0))),
((805 , 1411), (27119061, 32978753, 5.860, 0), ((1, 1), (2, 1))),
((1411, 1413), (32978753, 33013062, 0.034, 0), ((5, 1), (6, 1), (3, 1), (4, 1), (1, 0))),
((1411, 1413), (32978753, 33013062, 0.034, 0), ((1, 1), (2, 1))),
((1411, 1413), (32978753, 33013062, 0.034, 0), ((0, 1), (3, 0), (6, 0), (4, 0))),
((1411, 1413), (32978753, 33013062, 0.034, 0), ((0, 0), (5, 0))),
((1413, 1978), (33013062, 37228277, 4.215, 0), ((5, 1), (6, 1), (3, 1), (4, 1), (1, 0))),
((1413, 1978), (33013062, 37228277, 4.215, 0), ((0, 1), (3, 0), (4, 0), (6, 0), (2, 0))),
((1413, 1978), (33013062, 37228277, 4.215, 0), ((1, 1), (2, 1))),
((1413, 1978), (33013062, 37228277, 4.215, 0), ((0, 0), (5, 0))),
((1978, 2019), (37228277, 37509844, 0.282, 0), ((1, 1), (2, 1))),
((1978, 2019), (37228277, 37509844, 0.282, 0), ((0, 1), (3, 0), (4, 0), (6, 0), (2, 0))),
((1978, 2019), (37228277, 37509844, 0.282, 0), ((5, 1), (6, 1), (3, 1), (1, 0))),
((1978, 2019), (37228277, 37509844, 0.282, 0), ((0, 0), (5, 0))),
((2019, 2551), (37509844, 45007348, 7.498, 0), ((0, 1), (3, 0), (4, 0), (6, 0), (2, 0))),
((2019, 2551), (37509844, 45007348, 7.498, 0), ((0, 0), (5, 0))),
((2019, 2551), (37509844, 45007348, 7.498, 0), ((5, 1), (6, 1), (3, 1), (1, 0))),
((2019, 2551), (37509844, 45007348, 7.498, 0), ((4, 1), (1, 1), (2, 1))),
((2551, 2569), (45007348, 45198494, 0.191, 0), ((0, 0), (5, 0))),
((2551, 2569), (45007348, 45198494, 0.191, 0), ((0, 1), (3, 0), (6, 0), (2, 0))),
((2551, 2569), (45007348, 45198494, 0.191, 0), ((5, 1), (6, 1), (3, 1), (1, 0))),
((2551, 2569), (45007348, 45198494, 0.191, 0), ((4, 1), (1, 1), (2, 1))),
((2569, 2650), (45198494, 45892433, 0.694, 0), ((0, 0), (5, 0), (4, 0))),
((2569, 2650), (45198494, 45892433, 0.694, 0), ((0, 1), (3, 0), (6, 0), (2, 0))),
((2569, 2650), (45198494, 45892433, 0.694, 0), ((5, 1), (6, 1), (3, 1), (1, 0))),
((2569, 2650), (45198494, 45892433, 0.694, 0), ((4, 1), (1, 1), (2, 1))),
((2650, 2657), (45892433, 45940934, 0.049, 0), ((0, 0), (5, 0), (4, 0))),
((2650, 2657), (45892433, 45940934, 0.049, 0), ((0, 1), (3, 0), (6, 0), (2, 0))),
((2650, 2657), (45892433, 45940934, 0.049, 0), ((5, 1), (6, 1), (3, 1), (1, 0))),
((2650, 2657), (45892433, 45940934, 0.049, 0), ((4, 1), (1, 1))),
((2657, 3215), (45940934, 51103692, 5.163, 0), ((5, 1), (6, 1), (3, 1), (1, 0), (2, 1))),
((2657, 3215), (45940934, 51103692, 5.163, 0), ((0, 1), (3, 0), (6, 0), (2, 0))),
((2657, 3215), (45940934, 51103692, 5.163, 0), ((0, 0), (5, 0), (4, 0))),
((2657, 3215), (45940934, 51103692, 5.163, 0), ((4, 1), (1, 1))),
((3215, 3218), (51103692, 51156934, 0.053, 0), ((5, 1), (6, 1), (3, 1), (1, 0), (2, 1))),
((3215, 3218), (51103692, 51156934, 0.053, 0), ((4, 1), (1, 1))),
((3215, 3218), (51103692, 51156934, 0.053, 0), ((0, 1), (3, 0))),
((3215, 3218), (51103692, 51156934, 0.053, 0), ((0, 0), (5, 0)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
assert_equal(segment_set.errors,
[[2162, 2162, 2162, 2162, 2162, 2162, 2162, 2162, 2162, 2162, 2846, 3202, 2846,
3202, 1092, 3202, 1092, 3202, 3, 1092, 3, 1092, 3, 1092, 3202, 3, 1092, 3202,
1092, 3202, 1092, 3202],
[0, 2, 0, 3, 0, 4, 0, 5, 0, 6, 1, 1, 2, 2, 1, 1, 3, 3, 1, 1, 4, 4, 1, 1, 1, 5, 5,
5, 1, 1, 6, 6]],
'Wrong genotype errors')
self.assertTrue(max(len(list(g)) for (_, g) in itertools.groupby(segment_set, lambda segment: segment.snp)) <= 4,
'Too many distinct haplotypes in nuclear family')
# Extract IBD segments of child's haplotype vs. sibs
segments_of_30 = SegmentSet(Segment(x.snp, x.samples - set([(0, 0), (0, 1), (1, 0), (1, 1)]), x.bp, error_snps=x.error_snps)
for x in segment_set if (3, 0) in x.samples)
segments_of_30.merge_consecutive()
assert_segments_almost_equal(segments_of_30,
[((0 , 4), (16484792, 17087656, 0.603, 0), ((3, 0),)),
((4 , 805), (17087656, 27119061, 10.031, 0), ((3, 0), (4, 0))),
((805 , 1413), (27119061, 33013062, 5.894, 0), ((3, 0), (6, 0), (4, 0))),
((1413, 2551), (33013062, 45007348, 11.994, 0), ((3, 0), (2, 0), (6, 0), (4, 0))),
((2551, 3215), (45007348, 51103692, 6.096, 0), ((3, 0), (2, 0), (6, 0))),
((3215, 3218), (51103692, 51156934, 0.053, 0), ((3, 0),))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
segments_of_31 = SegmentSet(Segment(x.snp, x.samples - set([(0, 0), (0, 1), (1, 0), (1, 1)]), x.bp, error_snps=x.error_snps)
for x in segment_set if (3, 1) in x.samples)
segments_of_31.merge_consecutive()
assert_segments_almost_equal(segments_of_31,
[((1 , 2), (17065079, 17075353, 0.010, 0), ((3, 1),)),
((2 , 301), (17075353, 20993766, 3.918, 0), ((6, 1), (3, 1), (2, 1))),
((301 , 576), (20993766, 25228375, 4.235, 0), ((3, 1), (2, 1))),
((600 , 1978), (25444874, 37228277, 11.783, 0), ((5, 1), (6, 1), (3, 1), (4, 1))),
((1978, 2657), (37228277, 45940934, 8.713, 0), ((5, 1), (6, 1), (3, 1))),
((2657, 3218), (45940934, 51156934, 5.216, 0), ((5, 1), (6, 1), (3, 1), (2, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
def test_ibd_segments_ibs(self):
'''Test locating IBD segments between distant individuals. No IBD posterior filter (IBS=>IBD).'''
relatives = self.__phased_sibs(self.s)
segment_set = im.idist.ibd_segments_with_relatives(
self.problem, self.s, relatives, self.params,
im.ibd_distant.prob_ibd_ibs)
segment_set.group_to_disjoint()
assert_segments_almost_equal(
segment_set,
[((0, 38), (16484792, 17561913, 1.077, 0), ((5, 1), (1, 0), (1, 1),
(2, 1))),
((38, 180), (17561913, 18562888, 1.001, 0), ((1, 0), (1, 1),
(2, 1))),
((180, 195), (18562888, 19030336, 0.467, 0), ((1, 0), (1, 1),
(5, 0), (2, 1))),
((195, 329), (19030336, 21242544, 2.212, 0), ((1, 0), (5, 0),
(2, 1))),
((329, 369), (21242544, 22485301, 1.243, 0), ((5, 1), (1, 0),
(5, 0), (2, 1))),
((369, 435), (22485301, 23627369, 1.142, 0), ((1, 0), (5, 0),
(2, 1))),
((435, 506), (23627369, 24235198, 0.608, 0), ((1, 0), (1, 1),
(5, 0), (2, 1))),
((506, 581), (24235198, 25304473, 1.069, 0),
((5, 1), (1, 0), (1, 1), (5, 0), (2, 1))),
((581, 865), (25304473, 27370273, 2.066, 0), ((1, 0), (1, 1),
(5, 0), (2, 1))),
((865, 1032), (27370273, 28120707, 0.750, 0),
((1, 0), (2, 1), (1, 1), (5, 0), (4, 0))),
((1032, 1037), (28120707, 28165334, 0.045, 0),
((5, 0), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((1037, 1109), (28165334, 29400515, 1.235, 0),
((5, 0), (5, 1), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((1109, 1138), (29400515, 29495373, 0.095, 0),
((1, 0), (2, 1), (1, 1), (5, 0), (4, 0))),
((1138, 1249), (29495373, 30864692, 1.369, 0),
((5, 0), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((1249, 1276), (30864692, 31207207, 0.343, 0),
((1, 0), (2, 1), (1, 1), (5, 0), (4, 0))),
((1276, 1460), (31207207, 33291742, 2.085, 0),
((5, 0), (5, 1), (1, 0), (1, 1), (2, 1), (4, 0))),
((1460, 1792), (33291742, 35344317, 2.053, 0),
((1, 0), (2, 1), (1, 1), (5, 0), (4, 0))),
((1792, 1934), (35344317, 36746079, 1.402, 0),
((5, 0), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((1934, 2008), (36746079, 37383809, 0.638, 0),
((1, 0), (2, 1), (1, 1), (5, 0), (4, 0))),
((2008, 2052), (37383809, 37977282, 0.593, 0),
((5, 0), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2052, 2068), (37977282, 38538246, 0.561, 0),
((5, 0), (5, 1), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2068, 2170), (38538246, 39988277, 1.450, 0),
((5, 0), (5, 1), (1, 0), (1, 1), (2, 1), (4, 0))),
((2170, 2187), (39988277, 40351438, 0.363, 0),
((1, 0), (2, 1), (1, 1), (5, 0), (4, 0))),
((2187, 2189), (40351438, 40395084, 0.044, 0),
((5, 0), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2189, 2269), (40395084, 42235352, 1.840, 0),
((5, 0), (5, 1), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2269, 2313), (42235352, 42919125, 0.684, 0),
((5, 0), (5, 1), (1, 0), (1, 1), (2, 1), (4, 0))),
((2313, 2314), (42919125, 42982572, 0.063, 0),
((5, 0), (5, 1), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2314, 2315), (42982572, 43013836, 0.031, 0),
((5, 0), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2315, 2393), (43013836, 44023173, 1.009, 0),
((5, 0), (5, 1), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2393, 2414), (44023173, 44101411, 0.078, 0),
((5, 0), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2414, 2598), (44101411, 45409136, 1.308, 0),
((1, 0), (2, 1), (1, 1), (5, 0), (4, 0))),
((2598, 2661), (45409136, 45972017, 0.563, 0), ((1, 0), (1, 1),
(2, 1), (4, 0))),
((2661, 2666), (45972017, 46060541, 0.089, 0),
((5, 1), (1, 0), (1, 1), (2, 1), (4, 0))),
((2666, 2744), (46060541, 47175815, 1.115, 0),
((5, 0), (5, 1), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((2744, 2779), (47175815, 47387316, 0.212, 0),
((5, 0), (5, 1), (1, 0), (1, 1), (2, 1), (4, 0))),
((2779, 2835), (47387316, 47786315, 0.399, 0),
((1, 0), (2, 1), (1, 1), (5, 0), (4, 0))),
((2835, 3043), (47786315, 49171641, 1.385, 0), ((1, 0), (1, 1),
(2, 1), (4, 0))),
((3043, 3178), (49171641, 50120525, 0.949, 0),
((5, 0), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0))),
((3178, 3218), (50120525, 51156934, 1.036, 0),
((5, 0), (5, 1), (1, 0), (4, 1), (1, 1), (2, 1), (4, 0)))],
decimal=3,
err_msg='Wrong IBD segments')
def test_ibd_segments_hmm(self):
'''Test locating IBD segments between the unphased proband and its sib surrogate parents.
Uses HMM IBD posterior.'''
relatives = self.__phased_sibs(self.s)
segment_set = im.idist.ibd_segments_with_relatives(
self.problem, self.s, relatives, PhaseParam(debug=False),
im.ibd_hmm.prob_ibd_hmm)
segment_set.group_to_disjoint()
assert_segments_almost_equal(
segment_set,
[((0, 96), (16484792, 17948473, 1.464, 0), ((2, 0), (3, 1), (4, 1),
(2, 1))),
((96, 344), (17948473, 21460008, 3.512, 0), ((3, 1), (4, 1),
(2, 1))),
((344, 380), (21460008, 22554306, 1.094, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((380, 383), (22554306, 22555078, 0.001, 0), ((3, 1), (4, 1),
(2, 1))),
((383, 438), (22555078, 23636541, 1.081, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((438, 442), (23636541, 23695404, 0.059, 0), ((3, 1), (4, 1),
(2, 1))),
((442, 519), (23695404, 24406778, 0.711, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((519, 557), (24406778, 25088629, 0.682, 0),
((0, 1), (2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((557, 951), (25088629, 27698217, 2.610, 0), ((0, 1), (3, 1),
(4, 1), (2, 1))),
((951, 969), (27698217, 27832985, 0.135, 0),
((0, 1), (2, 0), (3, 1), (4, 1), (2, 1))),
((969, 1019), (27832985, 28093392, 0.260, 0), ((2, 0), (3, 1),
(4, 1), (2, 1))),
((1019, 1147), (28093392, 29670939, 1.578, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((1147, 1188), (29670939, 30113960, 0.443, 0), ((2, 0), (3, 1),
(4, 1), (2, 1))),
((1188, 1403), (30113960, 32950053, 2.836, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((1403, 1943), (32950053, 36891858, 3.942, 0), ((2, 0), (3, 1),
(4, 1), (2, 1))),
((1943, 2053), (36891858, 37982012, 1.090, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((2053, 2055), (37982012, 38086574, 0.105, 0), ((2, 0), (3, 1),
(4, 1), (2, 1))),
((2055, 2133), (38086574, 39454432, 1.368, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((2133, 2174), (39454432, 40018212, 0.564, 0), ((2, 0), (3, 1),
(4, 1), (2, 1))),
((2174, 2221), (40018212, 41107688, 1.089, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((2221, 2612), (41107688, 45515269, 4.408, 0), ((2, 0), (3, 1),
(4, 1), (2, 1))),
((2612, 2661), (45515269, 45972017, 0.457, 0),
((2, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((2661, 2735), (45972017, 47094390, 1.122, 0),
((0, 1), (0, 0), (3, 1), (2, 1), (2, 0), (1, 0), (4, 1), (1, 1),
(4, 0))),
((2735, 2945), (47094390, 48569604, 1.475, 0),
((2, 0), (0, 0), (1, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((2945, 2991), (48569604, 48741583, 0.172, 0),
((2, 0), (0, 0), (1, 0), (3, 1), (4, 1), (4, 0))),
((2991, 3127), (48741583, 49752332, 1.011, 0),
((2, 0), (0, 0), (1, 0), (3, 1), (4, 1), (2, 1), (4, 0))),
((3127, 3177), (49752332, 50120255, 0.368, 0),
((2, 0), (1, 0), (3, 1), (4, 1), (0, 0))),
((3177, 3218), (50120255, 51156934, 1.037, 0),
((0, 1), (0, 0), (3, 1), (2, 1), (2, 0), (1, 0), (4, 1), (1, 1),
(4, 0)))],
decimal=3,
err_msg='Wrong IBD segments')
def test_ibd_segments(self):
'''Test locating IBD segments between distant individuals..'''
segment_set = im.ibd_distant.ibd_segments_with_surrogate_parents(self.problem, 14, 1, 6, params=im.PhaseParam(debug=False),
prob_ibd_calculator=im.ibd_hmm.prob_ibd_hmm)
segment_set.group_to_disjoint()
assert_segments_almost_equal(segment_set,
[((0 , 76), (16484792, 17844295, 1.360, 0), ((16, 1), (16, 0), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((0 , 76), (16484792, 17844295, 1.360, 0), ((5, 1), (14, 1), (5, 0))),
((76 , 90), (17844295, 17909524, 0.065, 0), ((16, 1), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((76 , 90), (17844295, 17909524, 0.065, 0), ((5, 1), (14, 1), (5, 0))),
((90 , 95), (17909524, 17930263, 0.021, 0), ((16, 1), (16, 0), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((90 , 95), (17909524, 17930263, 0.021, 0), ((5, 1), (14, 1), (5, 0))),
((95 , 96), (17930263, 17948473, 0.018, 0), ((16, 1), (16, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((95 , 96), (17930263, 17948473, 0.018, 0), ((5, 1), (14, 1), (5, 0))),
((96 , 100), (17948473, 17987962, 0.039, 0), ((16, 1), (16, 0), (14, 0), (1, 1))),
((100 , 226), (17987962, 19486391, 1.498, 0), ((16, 1), (16, 0), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((100 , 226), (17987962, 19486391, 1.498, 0), ((5, 1), (14, 1), (5, 0))),
((226 , 251), (19486391, 19787736, 0.301, 0), ((16, 0), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((226 , 251), (19486391, 19787736, 0.301, 0), ((5, 1), (14, 1), (5, 0))),
((251 , 275), (19787736, 20075858, 0.288, 0), ((16, 1), (16, 0), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((251 , 275), (19787736, 20075858, 0.288, 0), ((5, 1), (14, 1), (5, 0))),
((275 , 279), (20075858, 20742450, 0.667, 0), ((16, 1), (1, 0), (14, 0))),
((279 , 300), (20742450, 20993519, 0.251, 0), ((16, 1), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((279 , 300), (20742450, 20993519, 0.251, 0), ((5, 1), (14, 1), (5, 0))),
((300 , 380), (20993519, 22554306, 1.561, 0), ((16, 1), (16, 0), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((300 , 380), (20993519, 22554306, 1.561, 0), ((5, 1), (14, 1), (5, 0))),
((380 , 383), (22554306, 22555078, 0.001, 0), ((16, 1), (1, 0), (23, 1), (1, 1), (14, 0))),
((380 , 383), (22554306, 22555078, 0.001, 0), ((14, 1), (5, 0))),
((383 , 385), (22555078, 22583252, 0.028, 0), ((16, 1), (16, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((383 , 385), (22555078, 22583252, 0.028, 0), ((14, 1), (5, 0))),
((385 , 401), (22583252, 23275227, 0.692, 0), ((16, 1), (16, 0), (23, 0), (14, 0), (23, 1), (1, 0), (1, 1))),
((385 , 401), (22583252, 23275227, 0.692, 0), ((5, 1), (14, 1), (5, 0))),
((401 , 444), (23275227, 23753059, 0.478, 0), ((0, 1), (16, 1), (16, 0), (23, 0), (14, 0), (23, 1), (24, 1), (1, 0), (1, 1))),
((401 , 444), (23275227, 23753059, 0.478, 0), ((5, 1), (14, 1), (5, 0))),
((444 , 454), (23753059, 23834889, 0.082, 0), ((0, 1), (16, 1), (23, 0), (14, 0), (23, 1), (24, 1), (1, 0), (1, 1))),
((444 , 454), (23753059, 23834889, 0.082, 0), ((5, 1), (14, 1), (5, 0))),
((454 , 466), (23834889, 23877733, 0.043, 0), ((0, 1), (23, 0), (14, 0), (23, 1), (24, 1), (1, 0), (1, 1))),
((454 , 466), (23834889, 23877733, 0.043, 0), ((5, 1), (14, 1), (5, 0))),
((466 , 499), (23877733, 24209759, 0.332, 0), ((0, 1), (27, 1), (0, 0), (23, 0), (14, 0), (23, 1), (24, 1), (1, 0), (24, 0), (1, 1))),
((466 , 499), (23877733, 24209759, 0.332, 0), ((5, 1), (14, 1), (5, 0))),
((499 , 570), (24209759, 25205719, 0.996, 0), ((0, 1), (27, 1), (0, 0), (14, 0), (23, 1), (24, 1), (1, 0), (24, 0), (1, 1))),
((499 , 570), (24209759, 25205719, 0.996, 0), ((14, 1), (5, 0))),
((570 , 582), (25205719, 25305370, 0.100, 0), ((0, 1), (27, 0), (27, 1), (0, 0), (14, 0), (23, 1), (24, 1), (1, 0), (24, 0), (1, 1))),
((570 , 582), (25205719, 25305370, 0.100, 0), ((14, 1), (5, 0))),
((582 , 584), (25305370, 25319244, 0.014, 0), ((0, 1), (27, 0), (27, 1), (0, 0), (14, 0), (23, 1), (24, 1), (24, 0))),
((582 , 584), (25305370, 25319244, 0.014, 0), ((14, 1), (5, 0))),
((584 , 674), (25319244, 26234080, 0.915, 0), ((0, 1), (27, 0), (27, 1), (7, 1), (0, 0), (14, 0), (23, 1), (24, 1), (24, 0))),
((584 , 674), (25319244, 26234080, 0.915, 0), ((14, 1), (5, 0))),
((674 , 679), (26234080, 26250271, 0.016, 0), ((0, 1), (27, 1), (7, 1), (0, 0), (14, 0), (23, 1), (24, 1), (24, 0))),
((674 , 679), (26234080, 26250271, 0.016, 0), ((14, 1), (5, 0))),
((679 , 700), (26250271, 26380870, 0.131, 0), ((0, 1), (0, 0), (26, 1), (7, 1), (27, 1), (14, 0), (23, 1), (24, 1), (24, 0))),
((679 , 700), (26250271, 26380870, 0.131, 0), ((14, 1), (5, 0))),
((700 , 710), (26380870, 26496622, 0.116, 0), ((0, 1), (14, 0), (26, 1), (7, 1), (24, 1), (23, 1))),
((700 , 710), (26380870, 26496622, 0.116, 0), ((14, 1), (5, 0))),
((710 , 1008), (26496622, 28019908, 1.523, 0), ((0, 1), (9, 1), (26, 1), (7, 1), (24, 1), (23, 1), (14, 0))),
((710 , 1008), (26496622, 28019908, 1.523, 0), ((14, 1), (5, 0))),
((1008, 1032), (28019908, 28120707, 0.101, 0), ((0, 1), (7, 0), (9, 1), (26, 1), (7, 1), (14, 0), (23, 1), (24, 1))),
((1008, 1032), (28019908, 28120707, 0.101, 0), ((14, 1), (5, 0))),
((1032, 1039), (28120707, 28169949, 0.049, 0), ((0, 1), (7, 0), (9, 1), (26, 1), (7, 1), (23, 0), (14, 0), (23, 1), (24, 1))),
((1032, 1039), (28120707, 28169949, 0.049, 0), ((5, 1), (14, 1), (5, 0))),
((1039, 1088), (28169949, 29130300, 0.960, 0), ((0, 1), (9, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1))),
((1039, 1088), (28169949, 29130300, 0.960, 0), ((5, 1), (14, 1), (5, 0))),
((1088, 1091), (29130300, 29145539, 0.015, 0), ((0, 1), (9, 0), (0, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1))),
((1088, 1091), (29130300, 29145539, 0.015, 0), ((5, 1), (14, 1), (5, 0))),
((1091, 1123), (29145539, 29465677, 0.320, 0), ((0, 1), (9, 0), (0, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1))),
((1091, 1123), (29145539, 29465677, 0.320, 0), ((14, 1), (5, 0))),
((1123, 1146), (29465677, 29661341, 0.196, 0), ((0, 1), (9, 0), (0, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1))),
((1123, 1146), (29465677, 29661341, 0.196, 0), ((14, 1), (5, 0))),
((1146, 1160), (29661341, 29834766, 0.173, 0), ((0, 1), (9, 0), (0, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1))),
((1146, 1160), (29661341, 29834766, 0.173, 0), ((14, 1), (5, 0))),
((1160, 1207), (29834766, 30433373, 0.599, 0), ((0, 1), (9, 0), (0, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1), (1, 1))),
((1160, 1207), (29834766, 30433373, 0.599, 0), ((14, 1), (5, 0))),
((1207, 1216), (30433373, 30575812, 0.142, 0), ((0, 1), (9, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1), (1, 1))),
((1207, 1216), (30433373, 30575812, 0.142, 0), ((14, 1), (5, 0))),
((1216, 1283), (30575812, 31288769, 0.713, 0), ((0, 1), (9, 0), (0, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1), (1, 1))),
((1216, 1283), (30575812, 31288769, 0.713, 0), ((14, 1), (5, 0))),
((1283, 1284), (31288769, 31323900, 0.035, 0), ((0, 1), (0, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1), (1, 1))),
((1283, 1284), (31288769, 31323900, 0.035, 0), ((14, 1), (5, 0))),
((1284, 1298), (31323900, 31546951, 0.223, 0), ((0, 1), (9, 0), (0, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1), (1, 1))),
((1284, 1298), (31323900, 31546951, 0.223, 0), ((14, 1), (5, 0))),
((1298, 1326), (31546951, 32210300, 0.663, 0), ((0, 1), (9, 0), (0, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1), (1, 0), (24, 0), (1, 1))),
((1298, 1326), (31546951, 32210300, 0.663, 0), ((5, 1), (14, 1), (5, 0))),
((1326, 1371), (32210300, 32683165, 0.473, 0), ((0, 1), (9, 0), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1), (1, 0), (24, 0), (1, 1))),
((1326, 1371), (32210300, 32683165, 0.473, 0), ((5, 1), (14, 1), (5, 0))),
((1371, 1385), (32683165, 32850349, 0.167, 0), ((0, 1), (9, 0), (9, 1), (26, 1), (7, 1), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1), (24, 0), (1, 1))),
((1371, 1385), (32683165, 32850349, 0.167, 0), ((5, 1), (14, 1), (5, 0))),
((1385, 1389), (32850349, 32878244, 0.028, 0), ((0, 1), (9, 1), (26, 1), (7, 1), (23, 0), (14, 0), (23, 1), (24, 1), (24, 0), (1, 1))),
((1385, 1389), (32850349, 32878244, 0.028, 0), ((5, 1), (14, 1), (5, 0))),
((1389, 1551), (32878244, 33995211, 1.117, 0), ((0, 1), (9, 1), (26, 1), (7, 1), (14, 0), (23, 1), (24, 1), (1, 1))),
((1389, 1551), (32878244, 33995211, 1.117, 0), ((14, 1), (5, 0))),
((1551, 1632), (33995211, 34523488, 0.528, 0), ((0, 1), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1), (1, 1))),
((1551, 1632), (33995211, 34523488, 0.528, 0), ((14, 1), (5, 0))),
((1632, 1798), (34523488, 35412768, 0.889, 0), ((0, 1), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (14, 0), (23, 1), (24, 1), (1, 1))),
((1632, 1798), (34523488, 35412768, 0.889, 0), ((14, 1), (5, 0))),
((1798, 1802), (35412768, 35440705, 0.028, 0), ((0, 1), (7, 0), (9, 1), (26, 1), (7, 1), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1), (24, 0), (1, 1))),
((1798, 1802), (35412768, 35440705, 0.028, 0), ((5, 1), (14, 1), (5, 0))),
((1802, 1864), (35440705, 35893156, 0.452, 0), ((0, 1), (7, 0), (9, 1), (26, 1), (7, 1), (23, 0), (14, 0), (23, 1), (24, 1), (24, 0), (1, 1))),
((1802, 1864), (35440705, 35893156, 0.452, 0), ((5, 1), (14, 1), (5, 0))),
((1864, 1948), (35893156, 36934821, 1.042, 0), ((0, 1), (23, 0), (14, 0), (26, 1), (23, 1), (24, 1), (24, 0))),
((1864, 1948), (35893156, 36934821, 1.042, 0), ((5, 1), (14, 1), (5, 0))),
((1948, 1986), (36934821, 37311806, 0.377, 0), ((0, 1), (0, 0), (26, 1), (23, 0), (14, 0), (23, 1), (24, 1), (24, 0))),
((1948, 1986), (36934821, 37311806, 0.377, 0), ((5, 1), (14, 1), (5, 0))),
((1986, 1994), (37311806, 37323988, 0.012, 0), ((0, 1), (0, 0), (14, 0), (26, 1), (23, 1), (24, 1))),
((1986, 1994), (37311806, 37323988, 0.012, 0), ((14, 1), (5, 0))),
((1994, 1998), (37323988, 37338286, 0.014, 0), ((0, 1), (0, 0), (14, 0), (26, 1), (23, 1), (24, 1), (26, 0))),
((1994, 1998), (37323988, 37338286, 0.014, 0), ((14, 1), (5, 0))),
((1998, 2000), (37338286, 37367308, 0.029, 0), ((0, 1), (0, 0), (26, 1), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1), (24, 0))),
((1998, 2000), (37338286, 37367308, 0.029, 0), ((5, 1), (14, 1), (5, 0))),
((2000, 2004), (37367308, 37375117, 0.008, 0), ((0, 1), (0, 0), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1), (24, 0))),
((2000, 2004), (37367308, 37375117, 0.008, 0), ((5, 1), (14, 1), (5, 0))),
((2004, 2087), (37375117, 38818676, 1.444, 0), ((0, 1), (0, 0), (26, 1), (26, 0), (23, 0), (14, 0), (23, 1), (24, 1), (24, 0))),
((2004, 2087), (37375117, 38818676, 1.444, 0), ((5, 1), (14, 1), (5, 0))),
((2087, 2093), (38818676, 38907849, 0.089, 0), ((26, 0), (14, 0), (26, 1))),
((2093, 2121), (38907849, 39197939, 0.290, 0), ((14, 0), (26, 1))),
((2129, 2219), (39320828, 41090009, 1.769, 0), ((26, 0), (14, 0))),
((2233, 2298), (41369108, 42654327, 1.285, 0), ((14, 0), (26, 1))),
((2298, 2462), (42654327, 44391234, 1.737, 0), ((26, 0), (14, 0), (26, 1))),
((2462, 2483), (44391234, 44557063, 0.166, 0), ((26, 0), (14, 0))),
((2483, 3108), (44557063, 49669972, 5.113, 0), ((26, 0), (14, 0), (26, 1))),
((3108, 3218), (49669972, 51156934, 1.487, 0), ((26, 0), (14, 0), (26, 1))),
((3108, 3218), (49669972, 51156934, 1.487, 0), ((14, 1), (6, 1)))],
decimal=3, err_msg='Wrong IBD segments')
