def tree_twoway_counts(tree, alphabet=DnaPairs, average=True, attr='Sequence'):
"""From tree, return dict of Count objects.
Note: if average is True, only has counts in m[i,j] or m[j,i], not both.
"""
leaves = list(tree.traverse())
result = {}
if average:
#return symmetric matrix
for first, second in two_item_combos(leaves):
seq_1 = getattr(first, attr)
seq_2 = getattr(second, attr)
result[(first.Id, second.Id)] = \
Counts.fromPair(seq_1, seq_2, alphabet)
else:
for first, second in two_item_combos(leaves):
seq_1 = getattr(first, attr)
seq_2 = getattr(second, attr)
result[(first.Id, second.Id)] = \
Counts.fromPair(seq_1, seq_2, alphabet,False)
result[(second.Id, first.Id)] = \
Counts.fromPair(seq_2, seq_1, alphabet,False)
return result
def tree_twoway_counts(tree, alphabet=DnaPairs, average=True, attr='Sequence'):
"""From tree, return dict of Count objects.
Note: if average is True, only has counts in m[i,j] or m[j,i], not both.
"""
leaves = list(tree.traverse())
result = {}
if average:
#return symmetric matrix
for first, second in two_item_combos(leaves):
seq_1 = getattr(first, attr)
seq_2 = getattr(second, attr)
result[(first.Id, second.Id)] = \
Counts.fromPair(seq_1, seq_2, alphabet)
else:
for first, second in two_item_combos(leaves):
seq_1 = getattr(first, attr)
seq_2 = getattr(second, attr)
result[(first.Id, second.Id)] = \
Counts.fromPair(seq_1, seq_2, alphabet,False)
result[(second.Id, first.Id)] = \
Counts.fromPair(seq_2, seq_1, alphabet,False)
return result
