def get_tree_iter(args, i):
"""
Reads in trees resulting from analyses of posterior predictive datasets.
"""
# Instantiates tree list
pp_trees = dendropy.TreeList()
file = args.basename + '_' + str(i)
try:
taxa = dendropy.TaxonSet()
if args.nruns > 1:
tree_file_paths = ['{file}_r{run}.t'.format(file = file, run = j) for j in range(1, args.nruns + 1)]
tree_iter = dendropy.multi_tree_source_iter(tree_file_paths, schema = 'nexus', taxon_set = taxa, tree_offset = args.burnin)
elif args.nruns == 1:
tree_file_path = '{file}_r1.t'.format(file = file)
tree_iter = dendropy.tree_source_iter(tree_file_path, schema = 'nexus', taxon_set = taxa, tree_offset = args.burnin)
except:
print '''
Problem getting tree iterator for {file}
Exiting...'''.format(file = file)
if args.debug:
traceback.print_exc()
sys.exit(1)
## Currently some error with the DataSet.unify_taxa() method [1.7.10]
# pp_trees.unify_taxa() # Just to make sure all trees share the same TaxonSet
# Returns a dataset object containing separate treelists for each pp dataset
return(tree_iter)
def tree_iter(infile,format,burnin,taxonset=None):
'''Returns an iterator over a multi-tree file.'''
return tree_source_iter(
stream=open(infile, 'rU'),
schema=format,
taxon_set=taxonset,
tree_offset=burnin)
def print_distances(tree_list,mle,uniq_flag=False):
mle_tree, taxa = get_mle_tree(mle)
distances = []
uniq_trees = dendropy.TreeList()
count = 1
for t in tree_source_iter(stream=open(tree_list, 'rU'),schema='nexus',taxon_set=taxa):
dist = treecalc.symmetric_difference(mle_tree, t)
print "Distance between MLE tree and tree %i: %i" % (count,dist)
distances.append(dist)
count +=1
if uniq_flag and dist > 0:
uniq_trees.append(t)
print("Mean symmetric distance between MLE and tree list: %d" \
% float(sum(distances)/len(distances)))
return uniq_trees, len(uniq_trees)
def print_distances(tree_list, mle, uniq_flag=False):
mle_tree, taxa = get_mle_tree(mle)
distances = []
uniq_trees = dendropy.TreeList()
count = 1
for t in tree_source_iter(stream=open(tree_list, 'rU'),
schema='nexus',
taxon_set=taxa):
dist = treecalc.symmetric_difference(mle_tree, t)
print "Distance between MLE tree and tree %i: %i" % (count, dist)
distances.append(dist)
count += 1
if uniq_flag and dist > 0:
uniq_trees.append(t)
print("Mean symmetric distance between MLE and tree list: %d" \
% float(sum(distances)/len(distances)))
return uniq_trees, len(uniq_trees)
#! /usr/bin/env python
import dendropy
from dendropy import tree_source_iter
from dendropy import treecalc
distances = []
taxa = dendropy.TaxonSet()
mle_tree = dendropy.Tree.get_from_path('pythonidae.mle.nex', 'nexus', taxon_set=taxa)
for mcmc_tree in tree_source_iter(
stream=open('pythonidae.mcmc.nex', 'rU'),
schema='nexus',
taxon_set=taxa,
tree_offset=200):
distances.append(treecalc.symmetric_difference(mle_tree, mcmc_tree))
print("Mean symmetric distance between MLE and MCMC trees: %d"
% float(sum(distances)/len(distances)))
#!/usr/bin/python import dendropy
from dendropy import tree_source_iter
best_tree = dendropy.Tree.get_from_path("best_tree.tre", schema="nexus")
output_f = open('treedist_output', 'w')
counter = 1
for tree in tree_source_iter(
stream=open('all_trees', 'rU'),
schema='nexus',
taxon_set=best_tree.taxon_set):
distance = best_tree.symmetric_difference(tree)
output_f.write("1 " + str(counter) + " " + str(distance) + "\n")
counter += 1
output_f.close()
def tree_iter(infile, format, burnin, taxonset=None):
'''Returns an iterator over a multi-tree file.'''
return tree_source_iter(stream=open(infile, 'rU'),
schema=format,
taxon_set=taxonset,
tree_offset=burnin)
def testSummaryTreeIter(self):
stream = pathmap.tree_source_stream('pythonidae.beast.summary.tre')
for tree in dendropy.tree_source_iter(stream, 'beast-summary-tree'):
self.verify_node_info(tree)