Created
October 21, 2020 15:42
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Convert scipy tree format to newick format (e.g. for working with figtree)
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from scipy.cluster import hierarchy | |
def tree2newick(node, newick, parentdist, leaf_names): | |
if node.is_leaf(): | |
return f"{leaf_names[node.id]}:{parentdist - node.dist:.2f}{newick}" | |
else: | |
if len(newick) > 0: | |
newick = f"):{parentdist - node.dist:.2f}{newick}" | |
else: | |
newick = ");" | |
newick = tree2newick(node.get_left(), newick, node.dist, leaf_names) | |
newick = tree2newick(node.get_right(), f",{newick}", node.dist, leaf_names) | |
newick = f"({newick}" | |
return newick | |
Z = linkage(dm, method="average") | |
tree = hierarchy.to_tree(Z, False) | |
newick = tree2newick(tree, "", tree.dist, leaf_names) |
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