def _test_branch_prior_predup(self):
"""Test branch prior"""
prep_dir("test/output/branch_prior_predup")
#out = open("test/output/branch_prior/flies.nt.approx.txt", "w")
out = sys.stderr
treeid = "predup"
tree = read_tree("test/data/flies.predup.tree")
drawTree(tree)
stree = read_tree("test/data/flies.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.param")
birth = .4
death = .39
pretime = 1.0
nsamples = 100
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
p = [
spidir.branch_prior(tree, stree, recon, events, params, birth,
death, pretime, nsamples, True)
for i in xrange(30)
]
p2 = [
spidir.branch_prior(tree, stree, recon, events, params, birth,
death, pretime, nsamples, False)
for i in xrange(30)
]
print >> out, "\t".join(
map(str,
[treeid, mean(p), sdev(p),
mean(p2), sdev(p2)]))
def _test_branch_prior_predup(self):
"""Test branch prior"""
prep_dir("test/output/branch_prior_predup")
# out = open("test/output/branch_prior/flies.nt.approx.txt", "w")
out = sys.stderr
treeid = "predup"
tree = read_tree("test/data/flies.predup.tree")
drawTree(tree)
stree = read_tree("test/data/flies.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.param")
birth = 0.4
death = 0.39
pretime = 1.0
nsamples = 100
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
p = [
spidir.branch_prior(tree, stree, recon, events, params, birth, death, pretime, nsamples, True)
for i in xrange(30)
]
p2 = [
spidir.branch_prior(tree, stree, recon, events, params, birth, death, pretime, nsamples, False)
for i in xrange(30)
]
print >> out, "\t".join(map(str, [treeid, mean(p), sdev(p), mean(p2), sdev(p2)]))
def _test_branch_prior_samples(self):
"""Test branch prior"""
prep_dir("test/output/branch_prior")
treeids = os.listdir("test/data/flies")
treeids = ["3"]
for treeid in treeids:
tree = read_tree("test/data/flies-duploss/%s/%s.tree" % (treeid, treeid))
print treeid
draw_tree(tree)
stree = read_tree("test/data/flies.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.param")
birth = 0.0012
death = 0.0013
pretime = 1.0
nsamples = 100
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
p = [
spidir.branch_prior(tree, stree, recon, events, params, birth, death, nsamples=nsamples, approx=True)
for i in xrange(30)
]
# row = [treeid,
# mean(p), exc_default(lambda: sdev(p), INF)]
print treeid, p
def test_search(self):
"""Test all terms"""
prep_dir("test/output/all_terms_search")
out = open("test/output/all_terms_search/flies.txt", "w")
#out = sys.stderr
treeids = os.listdir("test/data/flies")
#treeids = ["3"]
for treeid in treeids:
tree_correct = read_tree("test/data/flies.nt/%s/%s.tree" %
(treeid, treeid))
align = read_fasta("test/data/flies.nt/%s/%s.align" %
(treeid, treeid))
phylo.hash_order_tree(tree_correct)
print >>out, treeid
print >>out, "correct"
drawTree(tree_correct, out=out)
stree = read_tree("test/data/flies.norm.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.nt.param")
birth = .4
death = .39
pretime = 1.0
maxdoom = 20
bgfreq = [.258,.267,.266,.209]
kappa = 1.59
genes = align.keys()
seqs = align.values()
tree = spidir.search_climb(genes, seqs,
stree, gene2species,
params, birth, death, pretime,
bgfreq, kappa,
maxdoom=maxdoom,
niter=50, quickiter=100,
nsamples=100, branch_approx=True)
phylo.hash_order_tree(tree)
print >>out, "constructed"
drawTree(tree, out=out)
print >>out, "is_correct:", (phylo.hash_tree(tree) ==
phylo.hash_tree(tree_correct))
out.close()
def test_all_terms(self):
"""Test all terms"""
prep_dir("test/output/all_terms")
out = open("test/output/all_terms/flies.txt", "w")
#out = sys.stderr
treeids = os.listdir("test/data/flies")[:100]
#treeids = ["0"]
for treeid in treeids:
tree = read_tree("test/data/flies/%s/%s.nt.tree" %
(treeid, treeid))
align = read_fasta("test/data/flies/%s/%s.nt.align" %
(treeid, treeid))
print >> out, treeid
draw_tree(tree, out=out)
stree = read_tree("test/data/flies.norm.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.nt.param")
birth = .4
death = .39
pretime = 1.0
nsamples = 100
maxdoom = 20
bgfreq = [.258, .267, .266, .209]
kappa = 1.59
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
branchp, topp, seqlk = spidir.calc_joint_prob(align,
tree,
stree,
recon,
events,
params,
birth,
death,
pretime,
bgfreq,
kappa,
maxdoom=maxdoom,
terms=True)
joint = topp + branchp + seqlk
print >> out, "topp ", topp
print >> out, "branchp", branchp
print >> out, "seqlk ", seqlk
print >> out, "joint ", joint
out.close()
def optimize_model(self, gtree, stree, gene2species):
"""Optimizes the model"""
CostModel.optimize_model(self, gtree, stree, gene2species)
#=============================
# read sequences
if not self.align:
self.parser.error("--align must be specified")
self.align = fasta.read_fasta(self.align)
#=============================
# read SPIDIR parameters
if not self.params:
self.parser.error("--param must be specified")
self.params = spidir.read_params(self.params)
#=============================
# determine background base frequency
if self.bgfreq:
# use supplied frequency
vals = map(float, self.bgfreq.split(","))
if len(vals) != 4:
self.parser.error("invalid --bgfreq: %s" % self.bgfreq)
self.bgfreq = vals
else:
# compute frequency from alignment
self.bgfreq = alignlib.compute_bgfreq(self.align)
#=============================
# branch lengths
if self.kappa >= 0:
# use supplied kappa
self.kappa = self.kappa
else:
# compute kappa from alignment
# from spidir.find_ml_kapp_hky
minkappa = 0.4; maxkappa = 5.0; stepkappa = 0.1
maxlk = -util.INF
maxk = minkappa
for k in util.frange(minkappa, maxkappa, stepkappa):
l = spidir.find_ml_branch_lengths_hky(gtree, self.align, self.bgfreq, k, maxiter=1,
parsinit=(k == minkappa))
if l > maxlk:
maxlk = l
maxk = k
self.kappa = maxk
def test_all_terms(self):
"""Test all terms"""
prep_dir("test/output/all_terms")
out = open("test/output/all_terms/flies.txt", "w")
#out = sys.stderr
treeids = os.listdir("test/data/flies")[:100]
#treeids = ["0"]
for treeid in treeids:
tree = read_tree("test/data/flies/%s/%s.nt.tree" % (treeid, treeid))
align = read_fasta("test/data/flies/%s/%s.nt.align" % (treeid, treeid))
print >>out, treeid
draw_tree(tree, out=out)
stree = read_tree("test/data/flies.norm.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.nt.param")
birth = .4
death = .39
pretime = 1.0
nsamples = 100
maxdoom = 20
bgfreq = [.258,.267,.266,.209]
kappa = 1.59
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
branchp, topp, seqlk = spidir.calc_joint_prob(
align, tree, stree, recon, events, params,
birth, death, pretime,
bgfreq, kappa, maxdoom=maxdoom, terms=True)
joint = topp + branchp + seqlk
print >>out, "topp ", topp
print >>out, "branchp", branchp
print >>out, "seqlk ", seqlk
print >>out, "joint ", joint
out.close()
def _test_branch_prior_samples(self):
"""Test branch prior"""
prep_dir("test/output/branch_prior")
treeids = os.listdir("test/data/flies")
treeids = ["3"]
for treeid in treeids:
tree = read_tree("test/data/flies-duploss/%s/%s.tree" %
(treeid, treeid))
print treeid
draw_tree(tree)
stree = read_tree("test/data/flies.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.param")
birth = .0012
death = .0013
pretime = 1.0
nsamples = 100
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
p = [
spidir.branch_prior(tree,
stree,
recon,
events,
params,
birth,
death,
nsamples=nsamples,
approx=True) for i in xrange(30)
]
#row = [treeid,
# mean(p), exc_default(lambda: sdev(p), INF)]
print treeid, p
def _test_branch_prior_approx(self):
"""Test branch prior"""
prep_dir("test/output/branch_prior")
out = open("test/output/branch_prior/flies.approx.txt", "w")
out = sys.stderr
treeids = os.listdir("test/data/flies")
for treeid in treeids:
tree = read_tree("test/data/flies-duploss/%s/%s.nt.tree" % (treeid, treeid))
print treeid
draw_tree(tree)
stree = read_tree("test/data/flies.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.param")
birth = 0.0012
death = 0.0013
pretime = 1.0
nsamples = 100
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
p = [
spidir.branch_prior(tree, stree, recon, events, params, birth, death, nsamples=nsamples, approx=False)
for i in xrange(30)
]
p2 = [
spidir.branch_prior(tree, stree, recon, events, params, birth, death, nsamples=nsamples, approx=True)
for i in xrange(30)
]
row = [treeid, mean(p), exc_default(lambda: sdev(p), INF), mean(p2), exc_default(lambda: sdev(p2), INF)]
print >> out, "\t".join(map(str, row))
self.assert_(INF not in row and -INF not in row)
out.close()
def test_search(self):
"""Test all terms"""
prep_dir("test/output/all_terms_search")
out = open("test/output/all_terms_search/flies.txt", "w")
#out = sys.stderr
treeids = os.listdir("test/data/flies")
#treeids = ["3"]
for treeid in treeids:
tree_correct = read_tree("test/data/flies.nt/%s/%s.tree" %
(treeid, treeid))
align = read_fasta("test/data/flies.nt/%s/%s.align" %
(treeid, treeid))
phylo.hash_order_tree(tree_correct)
print >> out, treeid
print >> out, "correct"
drawTree(tree_correct, out=out)
stree = read_tree("test/data/flies.norm.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.nt.param")
birth = .4
death = .39
pretime = 1.0
maxdoom = 20
bgfreq = [.258, .267, .266, .209]
kappa = 1.59
genes = align.keys()
seqs = align.values()
tree = spidir.search_climb(genes,
seqs,
stree,
gene2species,
params,
birth,
death,
pretime,
bgfreq,
kappa,
maxdoom=maxdoom,
niter=50,
quickiter=100,
nsamples=100,
branch_approx=True)
phylo.hash_order_tree(tree)
print >> out, "constructed"
drawTree(tree, out=out)
print >> out, "is_correct:", (
phylo.hash_tree(tree) == phylo.hash_tree(tree_correct))
out.close()
def _test_branch_prior_approx(self):
"""Test branch prior"""
prep_dir("test/output/branch_prior")
out = open("test/output/branch_prior/flies.approx.txt", "w")
out = sys.stderr
treeids = os.listdir("test/data/flies")
for treeid in treeids:
tree = read_tree("test/data/flies-duploss/%s/%s.nt.tree" %
(treeid, treeid))
print treeid
draw_tree(tree)
stree = read_tree("test/data/flies.stree")
gene2species = phylo.read_gene2species("test/data/flies.smap")
params = spidir.read_params("test/data/flies.param")
birth = .0012
death = .0013
pretime = 1.0
nsamples = 100
recon = phylo.reconcile(tree, stree, gene2species)
events = phylo.label_events(tree, recon)
p = [
spidir.branch_prior(tree,
stree,
recon,
events,
params,
birth,
death,
nsamples=nsamples,
approx=False) for i in xrange(30)
]
p2 = [
spidir.branch_prior(tree,
stree,
recon,
events,
params,
birth,
death,
nsamples=nsamples,
approx=True) for i in xrange(30)
]
row = [
treeid,
mean(p),
exc_default(lambda: sdev(p), INF),
mean(p2),
exc_default(lambda: sdev(p2), INF)
]
print >> out, "\t".join(map(str, row))
self.assert_(INF not in row and -INF not in row)
out.close()