def main():
option_parser, options, args = parse_command_line_parameters(**script_info)
create_dir(options.output_dir, fail_on_exist=False)
master_tree, support_trees = load_tree_files(options.master_tree,
options.support_dir)
# get support of each node in master
new_master, bootstraps = bootstrap_support(master_tree, support_trees)
write_bootstrap_support_files(new_master, bootstraps, options.output_dir,
len(support_trees))
def main():
option_parser, options, args = parse_command_line_parameters(**script_info)
create_dir(options.output_dir, fail_on_exist=False)
master_tree, support_trees = load_tree_files(options.master_tree,
options.support_dir)
# get support of each node in master
new_master, bootstraps = bootstrap_support(master_tree, support_trees)
write_bootstrap_support_files(new_master, bootstraps, options.output_dir,
len(support_trees))
def test_bootstrap_support(self):
""" bootstrap_support should have correct bootstrap for a tree with
unlabeled internal nodes
"""
master_tree = parse_newick('((a:2,b:3):2,(c:1,d:2):7);')
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick('((a:6,b:8.2):2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33):2,d:7);') # abc are siblings
new_master, bootstraps = tc.bootstrap_support(master_tree, [t1, t2])
self.assertFloatEqual(sorted(bootstraps.values()),sorted([1.0, .5, .5]))
def test_bootstrap_support(self):
""" bootstrap_support should have correct bootstrap for a tree with
unlabeled internal nodes
"""
master_tree = parse_newick("((a:2,b:3):2,(c:1,d:2):7);")
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick("((a:6,b:8.2):2,(c:1,d:2):7);") # same structure
t2 = parse_newick("((a:2,b:3,c:33):2,d:7);") # abc are siblings
new_master, bootstraps = tc.bootstrap_support(master_tree, [t1, t2])
self.assertFloatEqual(sorted(bootstraps.values()), sorted([1.0, 0.5, 0.5]))
def test_bootstrap_support_labeled(self):
""" bootstrap_support should have correct bootstrap on a tree
with labeled internal nodes
"""
master_tree = parse_newick('((a:2,b:3)ab:2,(c:1,d:2)cd:7)rt;')
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick('((a:6,b:8.2)hi:2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33)ho:2,d:7);') # abc are siblings
new_master, bootstraps = tc.bootstrap_support(master_tree, [t1, t2])
expected = dict([('ab', .5),('cd',.5),('rt',1.0)])
self.assertFloatEqual(bootstraps, expected)
def test_bootstrap_support_labeled(self):
""" bootstrap_support should have correct bootstrap on a tree
with labeled internal nodes
"""
master_tree = parse_newick('((a:2,b:3)ab:2,(c:1,d:2)cd:7)rt;')
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick('((a:6,b:8.2)hi:2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33)ho:2,d:7);') # abc are siblings
new_master, bootstraps = tc.bootstrap_support(master_tree, [t1, t2])
expected = dict([('ab', .5), ('cd', .5), ('rt', 1.0)])
self.assertDictEqual(bootstraps, expected)
def test_bootstrap_support_subset(self):
""" bootstrap_support should have correct bootstrap on a tree
when one support tree is missing a tip
"""
master_tree = parse_newick("((a:2,b:3)ab:2,(c:1,d:2)cd:7)rt;")
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick("((a:6,b:8.2)hi:2,(c:1,d:2):7);") # same structure
t2 = parse_newick("((a:2,b:3,c:33)ho:2,d:7);") # abc are siblings
t3 = parse_newick("((a:6)hi:2,(c:1,d:2):7);") # b missing
t4 = parse_newick("(a:8,(c:1,d:2):7);") # b missing, and pruned
new_master, bootstraps = tc.bootstrap_support(master_tree, [t1, t2, t3, t4])
expected = dict([("cd", 0.75), ("rt", 1.0)])
self.assertFloatEqual(bootstraps, expected)
def test_bootstrap_support_subset(self):
""" bootstrap_support should have correct bootstrap on a tree
when one support tree is missing a tip
"""
master_tree = parse_newick('((a:2,b:3)ab:2,(c:1,d:2)cd:7)rt;')
"""
/-------.5 /-a
---1| \-b
\------.5 /-c
\-d
"""
t1 = parse_newick('((a:6,b:8.2)hi:2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33)ho:2,d:7);') # abc are siblings
t3 = parse_newick('((a:6)hi:2,(c:1,d:2):7);') # b missing
t4 = parse_newick('(a:8,(c:1,d:2):7);') # b missing, and pruned
new_master, bootstraps = tc.bootstrap_support(master_tree,
[t1, t2,t3,t4])
expected = dict([('cd',.75),('rt',1.0)])
self.assertFloatEqual(bootstraps, expected)
