class bayesianptp:
"""Run MCMC on multiple trees"""
def __init__(self, filename, ftype = "nexus", reroot = False, method = "H1", seed = 1234, thinning = 100, sampling = 10000, burnin = 0.1, firstktrees = 0, taxa_order = []):
self.method = method
self.seed = seed
self.thinning = thinning
self.sampling = sampling
self.burnin = burnin
self.firstktrees = firstktrees
if ftype == "nexus":
self.nexus = NexusReader(filename)
self.nexus.blocks['trees'].detranslate()
self.trees = self.nexus.trees.trees
else:
self.trees = self.raxmlTreeParser(filename)
if self.firstktrees > 0 and self.firstktrees <= len(self.trees):
self.trees = self.trees[:self.firstktrees]
self.taxa_order = taxa_order
if len(self.taxa_order) == 0:
self.taxa_order = Tree(self.trees[0]).get_leaf_names()
self.numtaxa = len(self.taxa_order)
self.numtrees = len(self.trees)
self.reroot = reroot
def remove_outgroups(self, ognames, remove = False, output = ""):
"""reroot using outgroups and remove them"""
self.reroot = False
try:
if remove:
for og in ognames:
self.taxa_order.remove(og)
self.numtaxa = len(self.taxa_order)
for i in range(len(self.trees)):
t = Tree(self.trees[i])
if len(ognames) < 2:
t.set_outgroup(ognames[0])
if remove:
t.prune(self.taxa_order, preserve_branch_length=True)
else:
ancestor = t.get_common_ancestor(ognames)
if not t == ancestor:
t.set_outgroup(ancestor)
if remove:
t.prune(self.taxa_order, preserve_branch_length=True)
self.trees[i] = t.write()
if remove and output!="":
with open(output, "w") as fout:
for t in self.trees:
fout.write(t + "\n")
except ValueError, e:
print(e)
print("")
print("")
print("Somthing is wrong with the input outgroup names")
print("")
print("Quiting .....")
sys.exit()
class bootstrap_ptp:
"""Run MCMC on multiple trees"""
def __init__(self,
filename,
ftype="nexus",
reroot=False,
method="H1",
firstktrees=0):
self.method = method
self.firstktrees = firstktrees
if ftype == "nexus":
self.nexus = NexusReader(filename)
self.nexus.blocks['trees'].detranslate()
self.trees = self.nexus.trees.trees
else:
self.trees = self.raxmlTreeParser(filename)
if self.firstktrees > 0 and self.firstktrees <= len(self.trees):
self.trees = self.trees[:self.firstktrees]
self.taxa_order = Tree(self.trees[0]).get_leaf_names()
self.numtaxa = len(self.taxa_order)
self.numtrees = len(self.trees)
self.reroot = reroot
def remove_outgroups(self, ognames, remove=False):
"""reroot using outgroups and remove them"""
self.reroot = False
try:
if remove:
for og in ognames:
self.taxa_order.remove(og)
self.numtaxa = len(self.taxa_order)
for i in range(len(self.trees)):
t = Tree(self.trees[i])
if len(ognames) < 2:
t.set_outgroup(ognames[0])
if remove:
t.prune(self.taxa_order, preserve_branch_length=True)
else:
ancestor = t.get_common_ancestor(ognames)
if not t == ancestor:
t.set_outgroup(ancestor)
if remove:
t.prune(self.taxa_order, preserve_branch_length=True)
self.trees[i] = t.write()
except ValueError, e:
print(e)
print(
"\n Somthing is wrong with the input outgroup names \n Quiting ..."
)
sys.exit()
class bootstrap_ptp:
"""Run MCMC on multiple trees"""
def __init__(self, filename, ftype="nexus", reroot=False, method="H1", firstktrees=0):
self.method = method
self.firstktrees = firstktrees
if ftype == "nexus":
self.nexus = NexusReader(filename)
self.nexus.blocks["trees"].detranslate()
self.trees = self.nexus.trees.trees
else:
self.trees = self.raxmlTreeParser(filename)
if self.firstktrees > 0 and self.firstktrees <= len(self.trees):
self.trees = self.trees[: self.firstktrees]
self.taxa_order = Tree(self.trees[0]).get_leaf_names()
self.numtaxa = len(self.taxa_order)
self.numtrees = len(self.trees)
self.reroot = reroot
def remove_outgroups(self, ognames, remove=False):
"""reroot using outgroups and remove them"""
self.reroot = False
try:
if remove:
for og in ognames:
self.taxa_order.remove(og)
self.numtaxa = len(self.taxa_order)
for i in range(len(self.trees)):
t = Tree(self.trees[i])
if len(ognames) < 2:
t.set_outgroup(ognames[0])
if remove:
t.prune(self.taxa_order, preserve_branch_length=True)
else:
ancestor = t.get_common_ancestor(ognames)
if not t == ancestor:
t.set_outgroup(ancestor)
if remove:
t.prune(self.taxa_order, preserve_branch_length=True)
self.trees[i] = t.write()
except ValueError, e:
print(e)
print("\n Somthing is wrong with the input outgroup names \n Quiting ...")
sys.exit()
class bayesianptp:
"""Run MCMC on multiple trees"""
def __init__(self,
filename,
ftype="nexus",
reroot=False,
method="H1",
seed=1234,
thinning=100,
sampling=10000,
burnin=0.1,
firstktrees=0,
taxa_order=[]):
self.method = method
self.seed = seed
self.thinning = thinning
self.sampling = sampling
self.burnin = burnin
self.firstktrees = firstktrees
if ftype == "nexus":
self.nexus = NexusReader(filename)
self.nexus.blocks['trees'].detranslate()
self.trees = self.nexus.trees.trees
else:
self.trees = self.raxmlTreeParser(filename)
if self.firstktrees > 0 and self.firstktrees <= len(self.trees):
self.trees = self.trees[:self.firstktrees]
self.taxa_order = taxa_order
if len(self.taxa_order) == 0:
self.taxa_order = Tree(self.trees[0]).get_leaf_names()
self.numtaxa = len(self.taxa_order)
self.numtrees = len(self.trees)
self.reroot = reroot
def remove_outgroups(self, ognames, remove=False, output=""):
"""reroot using outgroups and remove them"""
self.reroot = False
try:
if remove:
for og in ognames:
self.taxa_order.remove(og)
self.numtaxa = len(self.taxa_order)
for i in range(len(self.trees)):
t = Tree(self.trees[i])
if len(ognames) < 2:
t.set_outgroup(ognames[0])
if remove:
t.prune(self.taxa_order, preserve_branch_length=True)
else:
ancestor = t.get_common_ancestor(ognames)
if not t == ancestor:
t.set_outgroup(ancestor)
if remove:
t.prune(self.taxa_order, preserve_branch_length=True)
self.trees[i] = t.write()
if remove and output != "":
with open(output, "w") as fout:
for t in self.trees:
fout.write(t + "\n")
except ValueError, e:
print(e)
print("")
print("")
print("Somthing is wrong with the input outgroup names")
print("")
print("Quiting .....")
sys.exit()
