def gene2speciesArray(tree, stree, gene2species):
ptree, nodes, nodelookup = Spidir.makePtree(tree)
sptree, snodes, snodelookup = Spidir.makePtree(stree)
gene2speciesarray = []
for node in nodes:
if node.isLeaf():
gene2speciesarray.append(snodelookup[
stree.nodes[gene2species(node.name)]])
else:
gene2speciesarray.append(-1)
return gene2speciesarray
def gene2speciesArray(tree, stree, gene2species):
ptree, nodes, nodelookup = Spidir.makePtree(tree)
sptree, snodes, snodelookup = Spidir.makePtree(stree)
gene2speciesarray = []
for node in nodes:
if node.isLeaf():
gene2speciesarray.append(snodelookup[stree.nodes[gene2species(
node.name)]])
else:
gene2speciesarray.append(-1)
return gene2speciesarray
stree.nodes[gene2species(node.name)]])
else:
gene2speciesarray.append(-1)
return gene2speciesarray
tree = treelib.readTree("../data/0.nt.tree")
tree = treelib.parseNewick("((dmoj_sim,(dvir_sim,dgri_sim)),(dwil_sim,(dpse_sim,(dana_sim,(dmel_sim,(dyak_sim,dere_sim))))));")
tree = treelib.parseNewick("((dwil_sim,(dvir_sim,dgri_sim)),(dmoj_sim,(dpse_sim,(dana_sim,(dmel_sim,(dyak_sim,dere_sim))))));")
stree = treelib.readTree("../data/flies.stree")
gene2species = genomeutil.readGene2species("../data/flies.smap")
params = Spidir.readParams("../data/flies.nt.param")
ptree, nodes, nodelookup = Spidir.makePtree(tree)
pstree, snodes, snodelookup = Spidir.makePtree(stree)
g2s = gene2speciesArray(tree, stree, gene2species)
mu = [float(params[snode.name][0]) for snode in snodes]
sigma = [float(params[snode.name][1]) for snode in snodes]
alpha = float(params['baserate'][0])
beta = float(params['baserate'][1])
dists = pyspidir.genbranches(ptree, pstree, g2s, mu, sigma, alpha, beta)
for node, d in zip(nodes, dists):
node.dist = d
drawTree(tree)
print tree.root.children[0].dist
return gene2speciesarray
tree = treelib.readTree("../data/0.nt.tree")
tree = treelib.parseNewick(
"((dmoj_sim,(dvir_sim,dgri_sim)),(dwil_sim,(dpse_sim,(dana_sim,(dmel_sim,(dyak_sim,dere_sim))))));"
)
tree = treelib.parseNewick(
"((dwil_sim,(dvir_sim,dgri_sim)),(dmoj_sim,(dpse_sim,(dana_sim,(dmel_sim,(dyak_sim,dere_sim))))));"
)
stree = treelib.readTree("../data/flies.stree")
gene2species = genomeutil.readGene2species("../data/flies.smap")
params = Spidir.readParams("../data/flies.nt.param")
ptree, nodes, nodelookup = Spidir.makePtree(tree)
pstree, snodes, snodelookup = Spidir.makePtree(stree)
g2s = gene2speciesArray(tree, stree, gene2species)
mu = [float(params[snode.name][0]) for snode in snodes]
sigma = [float(params[snode.name][1]) for snode in snodes]
alpha = float(params['baserate'][0])
beta = float(params['baserate'][1])
dists = pyspidir.genbranches(ptree, pstree, g2s, mu, sigma, alpha, beta)
for node, d in zip(nodes, dists):
node.dist = d
drawTree(tree)
print tree.root.children[0].dist
