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_decorate_numtips(self):
"""decorate_numtips: decorate the number of tips below each node."""
obs = decorate_numtips(self.tree)
# make sure each tip only has 1 tip
tips = obs.tips()
for obs_tips in tips:
exp = 1
self.assertEqual(obs_tips.Score, exp)
# check that the node scores are correct
node_numtips = [1, 2, 8]
for nodes in obs:
self.assertTrue(nodes.Score in node_numtips)
def test_decorate_numtips(self):
"""decorate_numtips: decorate the number of tips below each node."""
obs = decorate_numtips(self.tree)
# make sure each tip only has 1 tip
tips = obs.tips()
for obs_tips in tips:
exp = 1
self.assertEqual(obs_tips.Score, exp)
# check that the node scores are correct
node_numtips = [1, 2, 8]
for nodes in obs:
self.assertTrue(nodes.Score in node_numtips)
