bam2clusters.py 文件源码

def array2tree(d, names, outbase="", method="ward"):
    """Return tree representation for array"""
    import ete3
    Z = fastcluster.linkage(d[np.triu_indices(d.shape[0], 1)], method=method)
    tree = sch.to_tree(Z, False)
    t = ete3.Tree(getNewick(tree, "", tree.dist, names))
    # save tree & newick
    if outbase:
        pdf, nw = outbase+".nw.pdf", outbase+".nw"
        with open(nw, "w") as out:
            out.write(t.write())

        ts = ete3.TreeStyle()
        ts.show_leaf_name = False
        ts.layout_fn = mylayout
        t.render(pdf, tree_style=ts)

    return t