def main():
args = parser.parse_args()
categories = args.categories
map_fp = args.map_fp
tree_fp = args.tree_fp
output_fp = args.output_fp
length = args.length
map_dict = parse_mapping_file_to_dict(map_fp)[0]
fields = categories.split(',')
tree = LoadTree(tree_fp)
furcated_tree = furcate_tree(tree, map_dict, fields, length=length)
tree.writeToFile(output_fp)
def main():
args = parser.parse_args()
categories = args.categories
map_fp = args.map_fp
tree_fp = args.tree_fp
output_fp = args.output_fp
length = args.length
map_dict = parse_mapping_file_to_dict(map_fp)[0]
fields = categories.split(',')
tree = LoadTree(tree_fp)
furcated_tree = furcate_tree(tree, map_dict, fields, length=length)
tree.writeToFile(output_fp)
from cogent import LoadTree
tree_f = argv[1]
taxa_f = open(argv[2], "U")
output_tree = argv[3]
taxa_depth = int(argv[4])
labels_map = {}
for line in taxa_f:
curr_label = line.split('\t')[0]
# Need to remove a number of characters that can interfere with tree loading/display
curr_taxa = ".".join(
(line.split('\t')[1].split(';')[0:taxa_depth])).replace(
' ', '').replace('(', '').replace(')',
'').replace(':', '').replace(
"'", '').replace('#', '')
labels_map[curr_label] = curr_taxa
tr = LoadTree(tree_f)
tips = tr.tips()
for curr_tip in tips:
curr_name = curr_tip.Name.replace(';', '')
curr_tip.Name = "%s;" % labels_map[curr_name]
tr.writeToFile(output_tree)
