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()
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 __init__(self, tree, sp_rate = 0, fix_sp_rate = False, max_iters = 20000, min_br = 0.0001):
self.min_brl = min_br
self.tree = Tree(tree, format = 1)
self.tree.resolve_polytomy(recursive=True)
self.tree.dist = 0.0
self.fix_spe_rate = fix_sp_rate
self.fix_spe = sp_rate
self.max_logl = float("-inf")
self.max_setting = None
self.null_logl = 0.0
self.null_model()
self.species_list = None
self.counter = 0
self.setting_set = set([])
self.max_num_search = max_iters
def __init__(self,
tree,
start_config=None,
reroot=False,
startmethod="H0",
min_br=0.0001,
seed=1234,
thinning=100,
sampling=10000,
burning=0.1,
taxa_order=[]):
if start_config == None:
me = exponential_mixture(tree=tree)
me.search(strategy=startmethod, reroot=reroot)
me.count_species(print_log=False, pv=0.0)
self.tree = me.tree
self.current_setting = me.max_setting
else:
self.current_setting = start_config
self.tree = Tree(tree, format=1)
self.burning = burning
self.last_setting = self.current_setting
self.current_logl = self.current_setting.get_log_l()
self.last_logl = self.last_setting.get_log_l()
self.min_br = min_br
self.rand_nr = random.Random()
self.rand_nr.seed(seed)
self.thinning = thinning
self.sampling = sampling
if taxa_order == []:
self.taxaorder = self.tree.get_leaf_names()
else:
self.taxaorder = taxa_order
self.numtaxa = len(self.taxaorder)
self.partitions = []
self.llhs = []
self.nsplit = 0
self.nmerge = 0
"""remember the ML partition"""
self.maxllh = self.current_logl
to, spe = self.current_setting.output_species(
taxa_order=self.taxaorder)
self.maxpar = spe
self.max_setting = self.current_setting
"""record all delimitation settings for plotting, this could consume a lot of MEM"""
self.settings = []
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
