def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
# get options
tree_fp = opts.input_tree
tips_to_keep = opts.tips_to_keep.split(',')
scoring_method = opts.scoring_method
# load tree
tree = DndParser(open(tree_fp, 'U'), constructor=PhyloNode)
# decorate measurements onto tree (either by depth or by number of children)
if scoring_method == 'depth':
tree2 = decorate_depth(tree)
elif scoring_method == 'numtips':
tree2 = decorate_numtips(tree)
# get the nodes for the inserted sequences
nodes_dict = get_insert_dict(tree2, set(tips_to_keep))
# remove nodes accordingly
final_tree = drop_duplicate_nodes(tree2, nodes_dict)
#final_tree.nameUnnamedNodes()
# write out the resulting tree
open_outpath = open(opts.output_fp, 'w')
open_outpath.write(final_tree.getNewick(with_distances=True))
open_outpath.close()
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
# get options
tree_fp= opts.input_tree
tips_to_keep=opts.tips_to_keep.split(',')
scoring_method=opts.scoring_method
# load tree
tree=DndParser(open(tree_fp,'U'), constructor=PhyloNode)
# decorate measurements onto tree (either by depth or by number of children)
if scoring_method=='depth':
tree2=decorate_depth(tree)
elif scoring_method=='numtips':
tree2=decorate_numtips(tree)
# get the nodes for the inserted sequences
nodes_dict = get_insert_dict(tree2, set(tips_to_keep))
# remove nodes accordingly
final_tree=drop_duplicate_nodes(tree2, nodes_dict)
#final_tree.nameUnnamedNodes()
# write out the resulting tree
open_outpath=open(opts.output_fp,'w')
open_outpath.write(final_tree.getNewick(with_distances=True))
open_outpath.close()
def test_drop_duplicate_nodes(self):
"""drop_duplicate_nodes: remove duplicate tips from tree based on either the number of tips or depth."""
# pull out the tips for Species006
inserted_nodes = get_insert_dict(self.tree, "Species006")
# decorate the depth of each node on the tree
decorated_tree = decorate_depth(self.tree)
# drop duplicate nodes based on depth (deterministic when equal depths)
obs = drop_duplicate_nodes(decorated_tree, inserted_nodes)
# verify the resulting tree is correct
self.assertEqual(obs.getNewick(with_distances=True), EXPECTED_TREE)
def test_get_insert_dict(self):
"""get_insert_dict: get the location of each inserted tip."""
# pull out the tips for Species006
obs = get_insert_dict(self.tree, "Species006")
# verify the dict is properly refrenced
self.assertTrue("Species006" in obs)
# if Species006 in dict, verify there are 3 tips
if "Species006" in obs:
exp_len = 3
obs_len = len(obs["Species006"])
self.assertEqual(obs_len, exp_len)
def test_drop_duplicate_nodes(self):
"""drop_duplicate_nodes: remove duplicate tips from tree based on either the number of tips or depth."""
# pull out the tips for Species006
inserted_nodes = get_insert_dict(self.tree, 'Species006')
# decorate the depth of each node on the tree
decorated_tree = decorate_depth(self.tree)
# drop duplicate nodes based on depth (deterministic when equal depths)
obs = drop_duplicate_nodes(decorated_tree, inserted_nodes)
# verify the resulting tree is correct
self.assertEqual(obs.getNewick(with_distances=True), EXPECTED_TREE)
def test_get_insert_dict(self):
"""get_insert_dict: get the location of each inserted tip."""
# pull out the tips for Species006
obs = get_insert_dict(self.tree, 'Species006')
# verify the dict is properly refrenced
self.assertTrue('Species006' in obs)
# if Species006 in dict, verify there are 3 tips
if 'Species006' in obs:
exp_len = 3
obs_len = len(obs['Species006'])
self.assertEqual(obs_len, exp_len)