def get_pairwise_dists(tree, mainsp):
"""get pairwise distances between the main taxon and the rest of the taxa"""
lst = []
for sp in tree.leaf_names():
lst.append((sp, treelib.find_dist(tree, mainsp, sp)))
lst.sort(key=lambda x: x[1])
names, dists = zip(*lst)
return names, dists
def get_pairwise_dists(tree, mainsp):
"""get pairwise distances between the main taxon and the rest of the taxa"""
lst = []
for sp in tree.leaf_names():
lst.append((sp, treelib.find_dist(tree, mainsp, sp)))
lst.sort(key=lambda x: x[1])
names, dists = zip(* lst)
return names, dists
def tree2distmat(tree, leaves):
"""Returns pair-wise distances between leaves of a tree"""
# TODO: not implemented efficiently
mat = []
for i in range(len(leaves)):
mat.append([])
for j in range(len(leaves)):
mat[-1].append(treelib.find_dist(tree, leaves[i], leaves[j]))
return mat
if __name__ == "__main__":
stree = treelib.read_tree('simple.stree')
popsize = 1e4
freq = 1e0
dr = 2.1
lr = 2.0
freqdup = .07
freqloss = .05
forcetime = 1e0
gtree = sim_tree(stree, popsize, freq, dr, lr, freqdup, freqloss, forcetime)
treelib.draw_tree(stree, scale=1)
print
for leaf in stree.leaves():
print leaf.name, treelib.find_dist(stree, stree.root.name, leaf.name)
print
treelib.draw_tree(gtree, scale=1)
print
if len(gtree.nodes) > 1:
for leaf in gtree.leaves():
print leaf.name, treelib.find_dist(gtree,gtree.root.name,leaf.name), leaf.data['freq']
else:
print 'only the root remains'
# if len(gtree.nodes) > 1:
# extant_count = 0
# for leaf in gtree.leaves():
# if leaf.data['freq'] > 0.0:
# extant_count += 1
