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
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
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"]))
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']))
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']))