def optimize_model(self, gtree, stree, gene2species):
"""Optimizes the model"""
CostModel.optimize_model(self, gtree, stree, gene2species)
# ensure gtree and stree are both rooted and binary
if not (treelib.is_rooted(gtree) and treelib.is_binary(gtree)):
raise Exception("gene tree must be rooted and binary")
if not (treelib.is_rooted(stree) and treelib.is_binary(stree)):
raise Exception("species tree must be rooted and binary")
try:
junk = phylo.reconcile(gtree, stree, gene2species)
except:
raise Exception("problem mapping gene tree to species tree")
treeout = StringIO.StringIO()
if not self.printed:
import pprint
treelib.draw_tree(gtree, out=treeout, minlen=5, maxlen=5)
print "gene tree:\n"
print(treeout.getvalue())
treelib.draw_tree(self.stree, out=treeout, minlen=5, maxlen=5)
print "spec tree:\n"
print(treeout.getvalue())
pprint.pprint(junk)
self.printed = True
def optimize_model(self, gtree, stree, gene2species):
"""Optimizes the model"""
CostModel.optimize_model(self, gtree, stree, gene2species)
# ensure gtree and stree are both rooted and binary
if not (treelib.is_rooted(gtree) and treelib.is_binary(gtree)):
raise Exception("gene tree must be rooted and binary")
if not (treelib.is_rooted(stree) and treelib.is_binary(stree)):
raise Exception("species tree must be rooted and binary")
try:
junk = phylo.reconcile(gtree, stree, gene2species)
except:
raise Exception("problem mapping gene tree to species tree")
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 optimize_model(self, gtree, stree, gene2species):
"""Optimizes the model"""
CostModel.optimize_model(self, gtree, stree, gene2species)
if self.dupcost < 0:
self.parser.error("-D/--dupcost must be >= 0")
if self.losscost < 0:
self.parser.error("-L/--losscost must be >= 0")
# ensure gtree and stree are both rooted and binary
if not (treelib.is_rooted(gtree) and treelib.is_binary(gtree)):
raise Exception("gene tree must be rooted and binary")
if not (treelib.is_rooted(stree) and treelib.is_binary(stree)):
raise Exception("species tree must be rooted and binary")
try:
junk = phylo.reconcile(gtree, stree, gene2species)
except:
raise Exception("problem mapping gene tree to species tree")
def optimize_model(self, gtree, stree, gene2species):
"""Optimizes the model"""
CostModel.optimize_model(self, gtree, stree, gene2species)
# check arguments
if self.dupcost < 0:
self.parser.error("-D/--dupcost must be >= 0: " + str(self.dupcost))
if self.losscost < 0:
self.parser.error("-L/--losscost must be >= 0: " + str(self.losscost))
if self.coalcost < 0:
self.parser.error("-C/--coalcost must be >= 0: " + str(self.coalcost))
if self.output is None:
self.parser.error("-o/--output must be specified")
if self.dcs < 0 or self.dcs > 1:
self.parser.error("--dcs must be in [0,1]: " + str(self.dcs))
# copy over tree topology
ltree = treelib.Tree(nextname=gtree.nextname)
def walk(node):
# copy of node
newnode = treelib.TreeNode(node.name)
# recurse
for child in node.children:
ltree.add_child(newnode, walk(child))
return newnode
if gtree.root:
walk(gtree.root)
ltree.root = ltree.nodes[gtree.root.name]
else:
raise Exception("input gene tree must be rooted")
self.locustree = ltree
# search functions
self.search = phylo.TreeSearchMix(None)
self.search.add_proposer(phylo.TreeSearchNni(None), 0.5)
self.search.add_proposer(phylo.TreeSearchSpr(None), 0.5)
