def test_match_maternal(self):
     '''Test hashing the rows of a haplotype matrix with the match() function. Here H is n x s.'''
     h_mat = ig._HapMatrix(self.problem, self.sibs, parent_type=MATERNAL)
     h = h_mat.h
     assert_equal(len(h_mat.snps), 2929, 'Wrong # filled snps')
     assert_equal(h.shape, (len(self.sibs), len(h_mat.snps)), 'Wrong extracted hap matrix size')
     assert_equal(self.ibd_computer._match(h[:, 0:10]), set([(1, 2)]), 'Wrong match set')
    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)')
Exemple #3
0
 def test_match(self):
     '''Test hashing the rows of a haplotype matrix with the match() function. Here H is n x s.'''
     h_mat = ig._HapMatrix(self.problem, self.sibs, parent_type=MATERNAL)
     h = h_mat.h
     assert_equal(len(h_mat.snps), 2915, 'Wrong # filled snps')
     assert_equal(h.shape, (len(self.sibs), len(h_mat.snps)),
                  'Wrong extracted hap matrix size')
     assert_equal(self.ibd_computer._match(h[:, 0:10]),
                  set([(1, 2), (1, 3), (2, 3)]), 'Wrong match set')
Exemple #4
0
 def test_match(self):
     '''Test hashing the rows of a haplotype matrix with the match() function.'''
     h_mat = ig._HapMatrix(self.problem, self.sibs)
     h = h_mat.h
     assert_equal(len(h_mat.snps), 3128, 'Wrong # filled snps')
     assert_equal(h.shape, (2 * len(self.sibs), len(h_mat.snps)),
                  'Wrong extracted hap matrix size')
     assert_equal(
         self.ibd_computer._match(h[:, 0:10]),
         set([(1, 3), (3, 7), (0, 6), (0, 9), (1, 5), (1, 7), (3, 5),
              (5, 7), (2, 4), (6, 9)]), 'Wrong match set')
Exemple #5
0
 def test_match(self):
     '''Test hashing the rows of a haplotype matrix with the match() function.'''
     h_mat = ig._HapMatrix(self.problem, self.sibs)
     h = h_mat.h
     assert_equal(len(h_mat.snps), 3128, 'Wrong # filled snps')
     assert_equal(h.shape, (2 * len(self.sibs), len(h_mat.snps)),
                  'Wrong extracted hap matrix size')
     assert_equal(self.ibd_computer._match(h[:, 0:10]),
                  set([(1, 3), (3, 7), (0, 6), (0, 9), (1, 5),
                       (1, 7), (3, 5), (5, 7), (2, 4), (6, 9)]),
                  'Wrong match set')
Exemple #6
0
 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_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)') 
Exemple #8
0
    def test_hash(self):
        '''Test hashing the rows of a haplotype matrix with the match() function. Here H is n x s.'''
        h_mat = ig._HapMatrix(self.problem, self.sibs, parent_type=MATERNAL)
        h = h_mat.h
        h = h[:, 0:10]
        assert_equal(h[1], h[2], 'These two test rows should be equal')
        def hash_array(x): x.tostring()
        assert_equal(hash_array(h[1]), hash_array(h[2]), 'Test objects should be equal, if not, rerun test')

        d = {}
        for (i, hi) in enumerate(h):
            d.setdefault(Hashable(hi), []).append(i)
        assert_equal(len(d), 2, 'Hashing haps into dictionary did not work')
Exemple #9
0
    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)')
Exemple #10
0
    def test_hash(self):
        '''Test hashing the rows of a haplotype matrix with the match() function. Here H is n x s.'''
        h_mat = ig._HapMatrix(self.problem, self.sibs, parent_type=MATERNAL)
        h = h_mat.h
        h = h[:, 0:10]
        assert_equal(h[1], h[2], 'These two test rows should be equal')

        def hash_array(x):
            x.tostring()

        assert_equal(hash_array(h[1]), hash_array(h[2]),
                     'Test objects should be equal, if not, rerun test')

        d = {}
        for (i, hi) in enumerate(h):
            d.setdefault(Hashable(hi), []).append(i)
        assert_equal(len(d), 2, 'Hashing haps into dictionary did not work')
Exemple #11
0
 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)') 
Exemple #12
0
 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)')
Exemple #13
0
 def test_parent_segments(self):
     '''Test computing GERMLINE IBD segments between the parents.'''
     m = self.ibd_computer.ibd_segments(
         ig._HapMatrix(self.problem,
                       self.family.parents)).group_to_disjoint()
     assert_equal(m.length, 0, 'Wrong best segment (IBD set size + length)')
 def test_parent_segments(self):
     '''Test computing GERMLINE IBD segments between the parents.'''
     m = self.ibd_computer.ibd_segments(ig._HapMatrix(self.problem, self.family.parents)).group_to_disjoint() 
     assert_equal(m.length, 0, 'Wrong best segment (IBD set size + length)') 
Exemple #15
0
    return d

def longest_segment(d): 
    return max([(snp, len(ibd)) for (snp,ibd) in d.iteritems()], key=operator.itemgetter(1))

def hash_ibd_list(ibd):
    return dict(((sample, i) for (i, samples) in enumerate(ibd) for sample in samples))

def highest_degree_node(ibd):
    return max([(i,len(ibd[hap_index[(i,0)]])+len(ibd[hap_index[(i,1)]])) for i in sibs], 
               key=operator.itemgetter(1))[0]

p = im.io.read_npz(itu.SIB_FOUNDERS_STAGE3)
f = p.families(genotyped=False)[0]
sibs = ig._filled_members(p, f) 
h_mat = ig._HapMatrix(p, sibs)
print h_mat
c = ig.GermlineIbdComputer()
segments = c.ibd_segments(h_mat)
segments.group_to_disjoint()
print segments

haps = set(itertools.product(sibs, ALLELES))
d = compress(segments, haps)
(best_segment, num_haps) = longest_segment(d)
print best_segment, num_haps
ibd = d[best_segment]
print ibd
hap_index = hash_ibd_list(ibd)
template = highest_degree_node(ibd)
print template