args = parser.parse_args() newick = args.tree[0] SPECIES_NAME_POS = args.species_field SPECIES_NAME_DELIMITER = args.species_delimiter # load a phylomeDB Tree provided as a newick file in the command line t = PhyloTree(newick, sp_naming_function=extract_spname) if args.root: if len(args.root) > 1: outgroup = t.get_common_ancestor(args.root) else: outgroup = t & args.root[0] t.set_outgroup(outgroup) if not args.skip_ortholog_detection: # detect speciation and duplication events using the species overlap # algorithm used in phylomeDB t.get_descendant_evol_events() if args.ascii: print t.get_ascii(attributes=[args.evoltype_attr, "name"], show_internal=True) if args.newick: print t.write(features=[args.evoltype_attr], format_root_node=True) if args.show: t.show()