#!/usr/bin/env python
from rasmus.common import *
from rasmus.bio import phylo
import Spidir
import Spidir.Likelihood
tree = readTree("../test/0.nt.tree")
stree = readTree("../test/flies.stree")
gene2species = genomeutil.readGene2species("../test/flies.smap")
params = Spidir.readParams("../test/flies.nt.param")
drawTree(tree)
print sum(x.dist for x in tree)
print Spidir.estGeneRate(tree, stree, params, gene2species)
print Spidir.estGeneRate(tree, stree, params, gene2species)
print Spidir.estGeneRate(tree, stree, params, gene2species)
print Spidir.Likelihood.getBaserate(tree, stree, params, gene2species=gene2species)
conf = {"python_only": True,
"famprob": True}
print Spidir.treeLogLikelihood(conf, tree, stree, gene2species, params)
conf = {}
#generate = Spidir.estGeneRate(tree, stree, params, gene2species)
for generate in frange(1.5, 2.3, .05):
print generate, Spidir.treeLogLikelihood(conf, tree, stree, gene2species, params,
baserate=generate)
#!/usr/bin/env python
from rasmus.common import *
from rasmus.bio import phylo
import Spidir
import Spidir.Likelihood
tree = readTree("../test/0.nt.tree")
stree = readTree("../test/flies.stree")
gene2species = genomeutil.readGene2species("../test/flies.smap")
params = Spidir.readParams("../test/flies.nt.param")
drawTree(tree)
print sum(x.dist for x in tree)
print Spidir.estGeneRate(tree, stree, params, gene2species)
print Spidir.estGeneRate(tree, stree, params, gene2species)
print Spidir.estGeneRate(tree, stree, params, gene2species)
print Spidir.Likelihood.getBaserate(tree,
stree,
params,
gene2species=gene2species)
conf = {"python_only": True, "famprob": True}
print Spidir.treeLogLikelihood(conf, tree, stree, gene2species, params)
conf = {}
#generate = Spidir.estGeneRate(tree, stree, params, gene2species)
for generate in frange(1.5, 2.3, .05):
print generate, Spidir.treeLogLikelihood(conf,
