def test_ibd_segments_sib_pair2(self):
'''Test calculating distant IBD segments against a single surrogate parent;
compare with IBD segments based on nucelar family info.'''
segment_set = ibd_segments_with_relatives(self.problem, 3, 5,
PhaseParam(id_coef_file=im.itu.ID_COEF_FILE, max_path_length=2),
im.ibd_hmm.prob_ibd_hmm)
im.itu.assert_segments_almost_equal(segment_set,
[((1278, 1337), (31217345, 32331594, 1.114, 1), ((3, 0), (5, 0))),
((2276, 2363), (42344297, 43527681, 1.183, 1), ((3, 1), (5, 0))),
((3138, 3206), (49803008, 50837224, 1.034, 1), ((3, 1), (5, 0))),
((603 , 3218), (25453554, 51156934, 25.703, 1), ((5, 1), (3, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
def test_ibd_segments_sib_pair(self):
'''Test calculating distant IBD segments between a pair of sibs;
compare with IBD segments based on nucelar family info'''
segment_set = ibd_segments_with_relatives(self.problem, 3, 2,
PhaseParam(id_coef_file=im.itu.ID_COEF_FILE),
im.ibd_hmm.prob_ibd_hmm)
im.itu.assert_segments_almost_equal(segment_set,
[((1412, 3218), (32992389, 51156934, 18.165, 1), ((3, 0), (2, 0))),
((241 , 451), (19643555, 23817486, 4.174, 1), ((2, 0), (3, 1))),
((0 , 600), (16484792, 25444874, 8.960, 1), ((3, 1), (2, 1))),
((2650, 3218), (45892433, 51156934, 5.265, 1), ((3, 1), (2, 1)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
def test_ibd_parent_vs_all_children(self):
'''Test calculating distant IBD segments against all surrogate parents;
compare with IBD segments based on nucelar family info.'''
# segment_set = ibd_segments_with_surrogate_parents(self.problem, 0,
# PhaseParam(margin=0., surrogate_parent_fill_threshold=0.9,
# max_path_length=2, debug=True),
# prob_ibd_calculator=im.ibd_hmm.prob_ibd_hmm,
# is_i_phased=True)
# Turn off kinship-based POO determination IBD segment computation since we don't have
# a complete pedigree here
segment_set = ibd_segments_with_relatives(self.problem, 0,
genotyped_children(self.problem, self.problem.first_family),
PhaseParam(id_coef_file=im.itu.ID_COEF_FILE, max_path_length=2),
im.ibd_hmm.prob_ibd_hmm, use_kinship=False)
im.itu.assert_segments_almost_equal(segment_set,
[((0 , 1420), (16484792, 33032458, 16.548, 1), ((2, 0), (0, 0))),
((241 , 446), (19643555, 23761236, 4.118, 1), ((0, 0), (2, 1))),
((2215, 2270), (40876234, 42241372, 1.365, 1), ((0, 0), (2, 1))),
((3138, 3206), (49803008, 50837224, 1.034, 1), ((0, 0), (2, 1))),
((1278, 1337), (31217345, 32331594, 1.114, 1), ((0, 1), (2, 0))),
((1411, 3218), (32978753, 51156934, 18.178, 1), ((0, 1), (2, 0))),
((1278, 1337), (31217345, 32331594, 1.114, 1), ((3, 0), (0, 0))),
((241 , 451), (19643555, 23817486, 4.174, 1), ((0, 0), (3, 1))),
((2276, 2363), (42344297, 43527681, 1.183, 1), ((0, 0), (3, 1))),
((3138, 3206), (49803008, 50837224, 1.034, 1), ((0, 0), (3, 1))),
((0 , 3218), (16484792, 51156934, 34.672, 1), ((0, 1), (3, 0))),
((1278, 1337), (31217345, 32331594, 1.114, 1), ((0, 0), (4, 0))),
((2552, 3218), (45011952, 51156934, 6.145, 1), ((0, 0), (4, 0))),
((385 , 451), (22583252, 23817486, 1.234, 1), ((0, 0), (4, 1))),
((2215, 2270), (40876234, 42241372, 1.365, 1), ((0, 0), (4, 1))),
((0 , 2571), (16484792, 45231758, 28.747, 1), ((0, 1), (4, 0))),
((0 , 3218), (16484792, 51156934, 34.672, 1), ((0, 0), (5, 0))),
((385 , 451), (22583252, 23817486, 1.234, 1), ((5, 1), (0, 0))),
((2276, 2363), (42344297, 43527681, 1.183, 1), ((5, 1), (0, 0))),
((3138, 3206), (49803008, 50837224, 1.034, 1), ((5, 1), (0, 0))),
((1278, 1337), (31217345, 32331594, 1.114, 1), ((0, 1), (5, 0))),
((0 , 805), (16484792, 27119061, 10.634, 1), ((0, 0), (6, 0))),
((1278, 1337), (31217345, 32331594, 1.114, 1), ((0, 0), (6, 0))),
((241 , 347), (19643555, 22015144, 2.372, 1), ((6, 1), (0, 0))),
((385 , 451), (22583252, 23817486, 1.234, 1), ((6, 1), (0, 0))),
((2276, 2363), (42344297, 43527681, 1.183, 1), ((6, 1), (0, 0))),
((3138, 3206), (49803008, 50837224, 1.034, 1), ((6, 1), (0, 0))),
((762 , 3218), (26836780, 51156934, 24.320, 1), ((0, 1), (6, 0)))],
full_data=True, decimal=3, err_msg='Wrong IBD segments')
