def test_parse_jackknife_support_file(self):
"""The jackknife support parser works"""
obs_dict = parse_jackknife_support_file(self.support_lines)
exp_dict = {
"trees_considered": 10,
"support_dict": {"node0": 1.0, "node1": 0.7, "node2": 0.4, "node3": 0.7, "node4": 0.6},
}
self.assertEqual(obs_dict, exp_dict)
def test_parse_jackknife_support_file(self):
"""The jackknife support parser works"""
obs_dict = parse_jackknife_support_file(self.support_lines)
exp_dict = {
'trees_considered': 10,
'support_dict': {
'node0': 1.0,
'node1': 0.7,
'node2': 0.4,
'node3': 0.7,
'node4': 0.6
}
}
self.assertEqual(obs_dict, exp_dict)
(0.7, 0.9): ("#82FF8B", "70-90%"),
(0.9, 0.999): ("#F8FE83", "90-99.9%"),
(0.999, None): ("#FF8582", "> 99.9%")
}
if __name__ == '__main__':
option_parser, opts, args = parse_command_line_parameters(**script_info)
support_fp = opts.support_fp
tree_fp = opts.tree_fp
mapping_fp = opts.mapping_fp
html_fp = opts.output_html_fp
output_dir = opts.output_dir
# Create output directory
try:
os.mkdir(output_dir)
except OSError:
pass
# Parse jackknife support file
support = parse_jackknife_support_file(open(support_fp, 'U'))
# Parse jackknife named nodes tree file
tree = parse_newick(open(tree_fp, 'U'), PhyloNode)
# Parse mapping file
mapping_data = parse_mapping_file_to_dict(open(mapping_fp, 'U'))
# Generate the html file
make_jackknife_tree_html_file(tree, support, DICT_TRANS_VALUES,
mapping_data, html_fp, output_dir)
