Example #1
0
def tree_threeway_counts(tree, lca_depths, alphabet=DnaPairs, attr='Sequence'):
    """From tree and array of lca_depths, returns n*n*n array of Count objects.

    n is number of leaves.

    lca_depths: array (leaf * leaf) of depths of last common ancestor.
    alphabet: pair alphabet for input sequences.

    Returns dict containing counts for (i, j, k) and (j, i, k) where k is the
    outgroup of the three sequences. Will pick an arbitrary node to be the
    outgroup if there is a polytomy.
    
    Note: Leaves of tree must have sequences already assigned.
    """
    outgroup_last = tree.outgroupLast
    leaves = list(tree.traverse())
    result = {}
    for first, second, third in three_item_combos(leaves):
        new_first, new_second, new_third = outgroup_last(first, second, third)
        #get the sequence from each node
        seq_1 = getattr(new_first, attr)
        seq_2 = getattr(new_second, attr)
        seq_3 = getattr(new_third, attr)

        result[(new_first.Id, new_second.Id, new_third.Id)] = \
            Counts.fromTriple(seq_1, seq_2, seq_3, alphabet)
        #don't forget to do counts from both  the non-outgroups
        result[(new_second.Id, new_first.Id, new_third.Id)] = \
            Counts.fromTriple(seq_2, seq_1, seq_3, alphabet)
    return result
Example #2
0
def tree_threeway_counts(tree, lca_depths, alphabet=DnaPairs, attr='Sequence'):
    """From tree and array of lca_depths, returns n*n*n array of Count objects.

    n is number of leaves.

    lca_depths: array (leaf * leaf) of depths of last common ancestor.
    alphabet: pair alphabet for input sequences.

    Returns dict containing counts for (i, j, k) and (j, i, k) where k is the
    outgroup of the three sequences. Will pick an arbitrary node to be the
    outgroup if there is a polytomy.
    
    Note: Leaves of tree must have sequences already assigned.
    """
    outgroup_last = tree.outgroupLast
    leaves = list(tree.traverse())
    result = {}
    for first, second, third in three_item_combos(leaves):
        new_first, new_second, new_third = outgroup_last(first, second, third)
        #get the sequence from each node
        seq_1 = getattr(new_first, attr)
        seq_2 = getattr(new_second, attr)
        seq_3 = getattr(new_third, attr)
        
        result[(new_first.Id, new_second.Id, new_third.Id)] = \
            Counts.fromTriple(seq_1, seq_2, seq_3, alphabet)
        #don't forget to do counts from both  the non-outgroups
        result[(new_second.Id, new_first.Id, new_third.Id)] = \
            Counts.fromTriple(seq_2, seq_1, seq_3, alphabet)
    return result
Example #3
0
 def test_three_item_combos(self):
     """three_item_combos should return items in correct order"""
     items = list(three_item_combos("abcde"))
     self.assertEqual(items, map(tuple, ["abc", "abd", "abe", "acd", "ace", "ade", "bcd", "bce", "bde", "cde"]))
Example #4
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 def test_three_item_combos(self):
     """three_item_combos should return items in correct order"""
     items = list(three_item_combos('abcde'))
     self.assertEqual(items, map(tuple, \
         ['abc','abd','abe','acd','ace','ade','bcd','bce','bde','cde']))
Example #5
0
 def test_three_item_combos(self):
     """three_item_combos should return items in correct order"""
     items = list(three_item_combos('abcde'))
     self.assertEqual(items, map(tuple, \
         ['abc','abd','abe','acd','ace','ade','bcd','bce','bde','cde']))