See -h help text with script for options. This script converts the tree tip IDs (OTU IDs) to the taxonomy strings that are in a supplied OTU table.

convert_tree_tips_to_taxa.py

#!/usr/bin/env

__author__ = "William Walters"
__copyright__ = "Copyright 2011"
__credits__ = ["William Walters"]
__license__ = "GPL"
__version__ = "1.0"
__maintainer__ = "William Walters"
__email__ = "William.A.Walters@gmail.com"

# USAGE: See help text with python convert_tree_tips_to_taxa.py -h
# This script will convert the OTU IDs in an input tree file to match the taxa strings
# in the paired OTU table.

from sys import argv
from os.path import basename, join

from biom import load_table
from skbio import TreeNode

from qiime.util import parse_command_line_parameters, get_options_lookup,\
 make_option, create_dir, qiime_open

options_lookup = get_options_lookup()
script_info={}
script_info['brief_description']="""This script will convert the OTU IDs in an input tree file to match the taxa strings in the paired OTU table."""
script_info['script_description']=""""""

script_info['output_description']="""A phylogenetic tree"""
script_info['required_options']= [\
    make_option('-i', '--otu_table_fp',type='existing_filepath',
                help='input OTU table'),
    make_option('-t', '--tree_fp',type='existing_filepath',
                help='input tree filepath'),
    options_lookup['output_dir']
]
script_info['optional_options']= [\
make_option('-d', '--taxa_depth',type='int', default=3,
                help='Depth of taxa to include in the output plot, e.g. 1=domain level')]
        
script_info['version'] = __version__
 
def main():
    option_parser, opts, args =\
        parse_command_line_parameters(suppress_verbose=True, **script_info)

    taxa_depth = opts.taxa_depth
    output_dir = opts.output_dir
    
    tip_taxa = {}
    otu_table = load_table(opts.otu_table_fp)
    tree = TreeNode.from_file(opts.tree_fp)
    create_dir(output_dir)
    
    obs_ids = set(otu_table._observation_ids)
    for x in obs_ids:
        tip_taxa[x] = "_".join(otu_table.metadata(x,\
            axis="observation")['taxonomy'][0:taxa_depth])
            
    
    output_tree_fp = join(output_dir + "/filtered_tree.tre")

    for tip in tree.tips():
        if tip.name in tip_taxa:
            tip.name = tip_taxa[tip.name]

    tree.write(output_tree_fp)

    
if __name__ == "__main__":
    main()