def buildTree(conf, stree, gene2species):
params = Spidir.readParams(conf["param"])
if "correcttree" in conf:
conf["correcthash"] = phylo.hash_tree(conf["correcttree"])
if "dist" in conf:
for i in range(len(conf["dist"])):
distfile = conf["dist"][i]
labels, distmat = phylip.read_dist_matrix(distfile)
# read in different labels if needed
if "labels" in conf:
labels = Spidir.readLabels(conf["labels"][i])
conf["aln"] = fasta.read_fasta(conf["labels"][i])
tree, logl = Spidir.spidir(conf, distmat, labels, stree,
gene2species, params)
tree.write(Spidir.outTreeFile(conf))
# test for correctness
if "correcttree" in conf:
correctTree = conf["correcttree"]
phylo.hash_order_tree(correctTree)
phylo.hash_order_tree(tree)
thash1 = phylo.hash_tree(tree)
thash2 = phylo.hash_tree(correctTree)
print "spidir: "
treelib.draw_tree(tree, maxlen=5, minlen=5)
print
print "correct:"
treelib.draw_tree(correctTree, maxlen=5, minlen=5)
print
if len(tree.leaves()) > 3:
rferror = Spidir.robinson_foulds_error(correctTree, tree)
else:
rferror = 0.0
if thash1 == thash2:
print "CORRECT TREE FOUND"
else:
print "WRONG TREE FOUND (RF: %f)" % rferror
#!/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)
for node in nodes:
if node.isLeaf():
gene2speciesarray.append(snodelookup[
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
#!/usr/bin/env python
from rasmus.common import *
from rasmus.bio import phylo
import Spidir
import spidir
tree = readTree("test/data/0.nt.tree")
stree = readTree("test/data/flies.stree")
gene2species = genomeutil.readGene2species("test/data/flies.smap")
params = Spidir.readParams("test/data/flies.nt.param")
aln = readFasta("test/data/1.nt.align")
bgfreqs = [.258,.267,.266,.209]
tsvratio = 1.59
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.Likelihood.getBaserate(tree, stree, params,
gene2species=gene2species)
#conf = {"python_only": True,
# "famprob": True}
#print Spidir.treeLogLikelihood(conf, tree, stree, gene2species, params)
util.tic("sample")
generates = spidir.sample_gene_rate(tree, stree, gene2species, params,
aln, bgfreqs, tsvratio, 20000)
#!/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,
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)
#!/usr/bin/env python
from rasmus.common import *
from rasmus.bio import phylo
import Spidir
import spidir
tree = readTree("test/data/0.nt.tree")
stree = readTree("test/data/flies.stree")
gene2species = genomeutil.readGene2species("test/data/flies.smap")
params = Spidir.readParams("test/data/flies.nt.param")
aln = readFasta("test/data/1.nt.align")
bgfreqs = [.258, .267, .266, .209]
tsvratio = 1.59
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.Likelihood.getBaserate(tree,
stree,
params,
gene2species=gene2species)
#conf = {"python_only": True,
# "famprob": True}
#print Spidir.treeLogLikelihood(conf, tree, stree, gene2species, params)
util.tic("sample")