#! /usr/bin/env python ############################################################################## ## DendroPy Phylogenetic Computing Library. ## ## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder. ## All rights reserved. ## ## See "LICENSE.rst" for terms and conditions of usage. ## ## If you use this work or any portion thereof in published work, ## please cite it as: ## ## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library ## for phylogenetic computing. Bioinformatics 26: 1569-1571. ## ############################################################################## """ Tests of parsimony scoring. """ import unittest import dendropy from dendropy.calculate import treescore from dendropy.test.support import pathmap class ParsimonyScoringTest(unittest.TestCase): def test_pscores_with_standard_data_and_gaps_as_new_states(self): # #NEXUS # begin paup; # set warnroot = no; # exe apternodus.chars.nexus; # gett file = apternodus.tre; # set criterion = parsimony; # pset gap = newstate; # pscore; # end; expected_scores = [396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 396, 713, 715, 723, 733, 672, 719, 734, 709, 695, 686] # begin paup; # set warnroot = no; # execute apternodus.chars.nexus; # gett file = apternodus.tre; # set crit=parsimony; # pset gap = newstate; # pscore / single = all scorefile=apternodus.gaps-as-newstate.scores.txt; # end; expected_per_site_scores = [ [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 2, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 5, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 2, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 3, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 6, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 5, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 5, 6, 4, 4, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 6, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 5, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 4, 2, 1, 2, 4, 4, 5, 5, 3, 4, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 3, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 6, 5, 6, 4, 5, 3, 3, 5, 2, 1, 3, 5, 1, 4, 3, 7, 6, 3, 4, 2, 3, 3, 5, 6, 5, 3, 2, 5, 5, 1, 5, 6, 7, 3, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 3, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [8, 13, 13, 4, 9, 12, 3, 4, 2, 4, 2, 2, 5, 6, 7, 2, 2, 3, 7, 7, 6, 8, 6, 7, 10, 10, 3, 7, 10, 3, 6, 8, 7, 7, 7, 4, 3, 7, 2, 7, 2, 4, 8, 9, 10, 13, 8, 6, 2, 7, 7, 5, 1, 2, 5, 7, 8, 8, 9, 6, 8, 10, 4, 9, 2, 1, 9, 7, 2, 6, 5, 11, 10, 9, 6, 3, 7, 8, 9, 7, 7, 6, 9, 9, 9, 2, 8, 9, 13, 4, 7, 9, 3, 2, 4, 6, 12, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 8, 4, 3, 4, 2, 2, 4, 4, 5, 3, 15,], [8, 12, 13, 4, 5, 12, 3, 4, 2, 4, 3, 2, 4, 6, 7, 2, 2, 3, 7, 6, 5, 8, 8, 9, 9, 10, 3, 8, 11, 3, 8, 8, 7, 7, 8, 4, 3, 7, 2, 7, 2, 4, 10, 11, 10, 13, 8, 6, 2, 6, 8, 5, 2, 3, 5, 8, 9, 8, 10, 5, 10, 10, 5, 9, 3, 1, 7, 6, 2, 7, 5, 10, 9, 8, 6, 3, 7, 6, 7, 7, 7, 6, 10, 9, 10, 2, 7, 7, 11, 4, 7, 10, 3, 3, 5, 6, 12, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 7, 4, 3, 4, 2, 1, 3, 3, 6, 3, 16,], [7, 12, 11, 4, 10, 10, 3, 4, 2, 4, 3, 2, 5, 7, 8, 2, 2, 3, 7, 5, 8, 10, 9, 9, 10, 8, 3, 9, 11, 3, 7, 6, 8, 8, 9, 4, 3, 7, 2, 6, 2, 4, 9, 7, 10, 12, 8, 6, 2, 6, 9, 5, 2, 3, 5, 7, 9, 10, 9, 5, 8, 11, 5, 9, 3, 1, 10, 6, 2, 7, 5, 11, 10, 9, 6, 3, 7, 8, 7, 7, 6, 6, 10, 7, 9, 2, 8, 8, 14, 4, 7, 10, 3, 3, 5, 7, 14, 6, 3, 4, 3, 4, 1, 2, 3, 5, 2, 6, 4, 3, 4, 2, 2, 5, 4, 5, 2, 14,], [8, 12, 11, 4, 9, 13, 3, 4, 2, 4, 3, 2, 5, 5, 7, 2, 2, 3, 7, 6, 7, 10, 9, 9, 10, 9, 3, 8, 10, 3, 7, 7, 6, 8, 9, 4, 2, 7, 2, 7, 2, 4, 11, 9, 8, 12, 9, 5, 2, 6, 9, 5, 2, 3, 5, 7, 9, 11, 7, 6, 9, 10, 5, 8, 3, 1, 8, 7, 2, 6, 5, 9, 11, 9, 6, 3, 8, 9, 8, 6, 6, 7, 9, 9, 10, 2, 9, 9, 14, 4, 7, 10, 3, 3, 5, 6, 11, 7, 4, 4, 3, 4, 3, 2, 3, 6, 2, 7, 4, 3, 4, 2, 2, 4, 5, 6, 3, 17,], [5, 7, 7, 3, 8, 9, 3, 4, 2, 3, 2, 2, 4, 4, 7, 2, 2, 3, 7, 4, 8, 9, 7, 7, 8, 10, 3, 7, 9, 3, 6, 5, 7, 6, 8, 4, 3, 6, 2, 6, 2, 4, 10, 6, 7, 13, 7, 5, 2, 6, 7, 5, 2, 3, 5, 6, 9, 9, 11, 5, 7, 12, 4, 8, 3, 1, 9, 5, 2, 7, 5, 9, 9, 8, 5, 3, 5, 9, 7, 7, 7, 6, 10, 8, 10, 2, 11, 9, 14, 4, 7, 9, 2, 3, 5, 6, 8, 4, 4, 4, 3, 5, 3, 2, 3, 5, 2, 7, 5, 3, 4, 2, 2, 4, 4, 6, 4, 14,], [7, 11, 12, 4, 8, 13, 3, 4, 2, 4, 3, 2, 5, 7, 8, 2, 2, 3, 7, 5, 5, 8, 9, 9, 10, 9, 3, 9, 10, 3, 8, 6, 9, 6, 8, 4, 3, 6, 2, 6, 2, 4, 9, 9, 9, 12, 8, 5, 2, 7, 9, 4, 2, 3, 5, 10, 9, 9, 9, 6, 10, 9, 5, 9, 3, 1, 10, 8, 2, 7, 5, 10, 9, 10, 6, 3, 7, 7, 7, 7, 7, 7, 8, 8, 8, 2, 7, 9, 13, 4, 7, 9, 3, 3, 5, 7, 14, 6, 4, 4, 3, 3, 3, 2, 3, 5, 2, 6, 3, 3, 4, 2, 2, 4, 5, 2, 4, 15,], [8, 12, 13, 4, 7, 12, 3, 4, 2, 4, 3, 2, 5, 6, 7, 2, 2, 3, 6, 5, 7, 9, 8, 8, 7, 8, 3, 8, 12, 3, 8, 8, 8, 8, 9, 3, 3, 7, 2, 7, 2, 4, 10, 8, 11, 11, 7, 5, 2, 7, 8, 5, 2, 3, 5, 8, 9, 9, 10, 6, 9, 12, 5, 11, 3, 1, 11, 8, 2, 7, 5, 11, 11, 8, 6, 3, 8, 5, 7, 7, 7, 6, 11, 8, 8, 2, 11, 9, 14, 4, 6, 11, 3, 3, 5, 6, 13, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 6, 4, 3, 4, 2, 2, 4, 5, 5, 4, 13,], [8, 11, 13, 3, 10, 12, 3, 4, 2, 4, 3, 2, 5, 4, 6, 2, 2, 3, 7, 6, 8, 9, 6, 6, 9, 9, 3, 8, 11, 3, 7, 8, 9, 7, 10, 4, 3, 6, 2, 6, 2, 4, 11, 9, 9, 11, 9, 6, 2, 6, 8, 4, 2, 3, 5, 8, 8, 9, 9, 6, 9, 10, 5, 8, 3, 1, 8, 7, 2, 5, 5, 9, 7, 8, 6, 3, 6, 6, 8, 7, 6, 7, 10, 9, 7, 2, 7, 9, 13, 4, 7, 10, 3, 3, 5, 7, 14, 6, 4, 4, 3, 5, 3, 2, 3, 4, 2, 6, 5, 3, 4, 2, 2, 4, 4, 3, 4, 15,], [6, 12, 11, 4, 9, 11, 3, 3, 2, 4, 3, 2, 3, 6, 7, 2, 2, 3, 6, 6, 9, 10, 9, 9, 10, 10, 3, 9, 11, 3, 7, 7, 6, 8, 7, 4, 3, 6, 1, 5, 2, 3, 9, 7, 8, 9, 8, 5, 2, 7, 8, 5, 2, 3, 5, 8, 9, 11, 8, 6, 8, 10, 5, 8, 3, 1, 6, 6, 2, 6, 5, 11, 8, 11, 6, 3, 8, 8, 7, 7, 7, 5, 9, 9, 10, 2, 7, 9, 11, 4, 7, 8, 3, 2, 4, 7, 13, 5, 4, 4, 2, 4, 2, 2, 2, 4, 2, 5, 4, 3, 4, 2, 2, 6, 5, 4, 3, 13,], [6, 9, 10, 4, 8, 12, 3, 3, 2, 4, 3, 2, 5, 6, 8, 2, 2, 3, 7, 6, 6, 8, 7, 7, 10, 6, 3, 6, 9, 3, 7, 7, 5, 8, 7, 4, 3, 6, 2, 6, 2, 3, 10, 9, 7, 11, 7, 6, 2, 6, 6, 5, 2, 3, 5, 8, 9, 8, 10, 6, 7, 11, 4, 8, 3, 1, 8, 6, 2, 7, 5, 10, 7, 10, 6, 3, 8, 8, 7, 6, 6, 7, 9, 8, 9, 2, 9, 9, 12, 4, 6, 10, 3, 3, 5, 5, 12, 6, 5, 4, 3, 5, 3, 2, 2, 4, 2, 7, 5, 3, 3, 2, 2, 5, 4, 5, 2, 16,], ] self.verify_pscores( trees_fname="apternodus.tre", chars_fname="apternodus.chars.nexus", matrix_type=dendropy.StandardCharacterMatrix, gaps_as_missing=False, expected_scores=expected_scores, expected_per_site_scores=expected_per_site_scores) def test_pscores_with_standard_data_and_gaps_as_missing(self): # #NEXUS # begin paup; # set warnroot = no; # exe apternodus.chars.nexus; # gett file = apternodus.tre; # set criterion = parsimony; # pset gap = missing; # pscore; # end; expected_scores = [ 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 370, 671, 670, 678, 687, 633, 675, 689, 668, 652, 644] # begin paup; # set warnroot = no; # execute apternodus.chars.nexus; # gett file = apternodus.tre; # set crit=parsimony; # pset gap = missing; # pscore / single = all scorefile=apternodus.gaps-as-missing.scores.txt; # end; expected_per_site_scores = [ [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 3, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 6, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 7, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 2, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 4, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 2, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 3, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 5, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 4, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 4, 5, 3, 4, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 5, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [4, 4, 3, 3, 5, 9, 2, 2, 1, 2, 3, 2, 3, 2, 1, 2, 1, 2, 4, 4, 5, 2, 3, 1, 5, 5, 2, 3, 7, 1, 1, 1, 3, 2, 3, 2, 1, 3, 1, 2, 1, 2, 7, 4, 3, 7, 2, 4, 1, 4, 3, 4, 1, 2, 4, 6, 5, 4, 5, 3, 5, 3, 3, 5, 2, 1, 3, 5, 1, 3, 2, 7, 6, 3, 4, 2, 3, 3, 4, 5, 4, 3, 2, 4, 5, 1, 5, 5, 6, 2, 3, 6, 2, 1, 4, 3, 5, 5, 3, 3, 2, 3, 2, 1, 2, 3, 1, 2, 3, 1, 2, 1, 2, 3, 3, 4, 1, 8,], [8, 13, 6, 4, 9, 12, 3, 4, 2, 4, 2, 2, 5, 6, 3, 2, 2, 3, 7, 7, 6, 3, 6, 1, 10, 10, 3, 7, 10, 3, 6, 8, 7, 7, 7, 4, 3, 7, 2, 5, 2, 4, 8, 9, 10, 13, 8, 6, 2, 7, 7, 5, 1, 2, 5, 7, 7, 7, 8, 5, 8, 10, 4, 9, 2, 1, 9, 7, 2, 4, 3, 11, 10, 9, 6, 3, 7, 8, 8, 6, 6, 6, 9, 7, 9, 2, 8, 8, 12, 3, 7, 9, 3, 2, 4, 6, 12, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 6, 4, 3, 4, 2, 2, 4, 4, 5, 3, 15,], [8, 12, 5, 4, 5, 12, 3, 4, 2, 4, 3, 2, 4, 6, 3, 2, 2, 3, 7, 6, 5, 3, 8, 1, 9, 10, 3, 8, 11, 3, 8, 8, 7, 7, 8, 4, 3, 7, 2, 5, 2, 4, 10, 11, 10, 13, 8, 6, 2, 6, 8, 5, 2, 3, 5, 8, 8, 7, 9, 4, 10, 10, 5, 9, 3, 1, 7, 6, 2, 5, 3, 10, 9, 8, 6, 3, 7, 6, 6, 6, 6, 6, 10, 7, 10, 2, 7, 6, 10, 3, 7, 10, 3, 3, 5, 6, 12, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 5, 4, 3, 4, 2, 1, 3, 3, 6, 3, 16,], [7, 12, 6, 4, 10, 10, 3, 4, 2, 4, 3, 2, 5, 7, 3, 2, 2, 3, 7, 5, 8, 3, 9, 1, 10, 8, 3, 9, 11, 3, 7, 6, 8, 8, 9, 4, 3, 7, 2, 4, 2, 4, 9, 7, 10, 12, 8, 6, 2, 6, 9, 5, 2, 3, 5, 7, 8, 9, 8, 4, 8, 11, 5, 9, 3, 1, 10, 6, 2, 5, 3, 11, 10, 9, 6, 3, 7, 8, 6, 6, 5, 6, 10, 5, 9, 2, 8, 7, 13, 3, 7, 10, 3, 3, 5, 7, 14, 6, 3, 4, 3, 4, 1, 2, 3, 5, 2, 4, 4, 3, 4, 2, 2, 5, 4, 5, 2, 14,], [8, 12, 4, 4, 9, 13, 3, 4, 2, 4, 3, 2, 5, 5, 3, 2, 2, 3, 7, 6, 7, 3, 9, 1, 10, 9, 3, 8, 10, 3, 7, 7, 6, 8, 9, 4, 2, 7, 2, 5, 2, 4, 11, 9, 8, 12, 9, 5, 2, 6, 9, 5, 2, 3, 5, 7, 8, 10, 6, 5, 9, 10, 5, 8, 3, 1, 8, 7, 2, 4, 3, 9, 11, 9, 6, 3, 8, 9, 7, 5, 5, 7, 9, 7, 10, 2, 9, 8, 13, 3, 7, 10, 3, 3, 5, 6, 11, 7, 4, 4, 3, 4, 3, 2, 3, 6, 2, 5, 4, 3, 4, 2, 2, 4, 5, 6, 3, 17,], [5, 7, 4, 3, 8, 9, 3, 4, 2, 3, 2, 2, 4, 4, 3, 2, 2, 3, 7, 4, 8, 3, 7, 1, 8, 10, 3, 7, 9, 3, 6, 5, 7, 6, 8, 4, 3, 6, 2, 4, 2, 4, 10, 6, 7, 13, 7, 5, 2, 6, 7, 5, 2, 3, 5, 6, 8, 8, 10, 4, 7, 12, 4, 8, 3, 1, 9, 5, 2, 5, 3, 9, 9, 8, 5, 3, 5, 9, 6, 6, 6, 6, 10, 6, 10, 2, 11, 8, 13, 3, 7, 9, 2, 3, 5, 6, 8, 4, 4, 4, 3, 5, 3, 2, 3, 5, 2, 5, 5, 3, 4, 2, 2, 4, 4, 6, 4, 14,], [7, 11, 6, 4, 8, 13, 3, 4, 2, 4, 3, 2, 5, 7, 3, 2, 2, 3, 7, 5, 5, 3, 9, 1, 10, 9, 3, 9, 10, 3, 8, 6, 9, 6, 8, 4, 3, 6, 2, 4, 2, 4, 9, 9, 9, 12, 8, 5, 2, 7, 9, 4, 2, 3, 5, 10, 8, 8, 8, 5, 10, 9, 5, 9, 3, 1, 10, 8, 2, 5, 3, 10, 9, 10, 6, 3, 7, 7, 6, 6, 6, 7, 8, 6, 8, 2, 7, 8, 12, 3, 7, 9, 3, 3, 5, 7, 14, 6, 4, 4, 3, 3, 3, 2, 3, 5, 2, 4, 3, 3, 4, 2, 2, 4, 5, 2, 4, 15,], [8, 12, 5, 4, 7, 12, 3, 4, 2, 4, 3, 2, 5, 6, 3, 2, 2, 3, 6, 5, 7, 3, 8, 1, 7, 8, 3, 8, 12, 3, 8, 8, 8, 8, 9, 3, 3, 7, 2, 5, 2, 4, 10, 8, 11, 11, 7, 5, 2, 7, 8, 5, 2, 3, 5, 8, 8, 8, 9, 5, 9, 12, 5, 11, 3, 1, 11, 8, 2, 5, 3, 11, 11, 8, 6, 3, 8, 5, 6, 6, 6, 6, 11, 6, 8, 2, 11, 8, 13, 3, 6, 11, 3, 3, 5, 6, 13, 7, 4, 4, 3, 4, 3, 2, 3, 5, 2, 4, 4, 3, 4, 2, 2, 4, 5, 5, 4, 13,], [8, 11, 5, 3, 10, 12, 3, 4, 2, 4, 3, 2, 5, 4, 3, 2, 2, 3, 7, 6, 8, 3, 6, 1, 9, 9, 3, 8, 11, 3, 7, 8, 9, 7, 10, 4, 3, 6, 2, 5, 2, 4, 11, 9, 9, 11, 9, 6, 2, 6, 8, 4, 2, 3, 5, 8, 7, 8, 8, 5, 9, 10, 5, 8, 3, 1, 8, 7, 2, 3, 3, 9, 7, 8, 6, 3, 6, 6, 7, 6, 5, 7, 10, 7, 7, 2, 7, 8, 12, 3, 7, 10, 3, 3, 5, 7, 14, 6, 4, 4, 3, 5, 3, 2, 3, 4, 2, 4, 5, 3, 4, 2, 2, 4, 4, 3, 4, 15,], [6, 12, 5, 4, 9, 11, 3, 3, 2, 4, 3, 2, 3, 6, 3, 2, 2, 3, 6, 6, 9, 3, 9, 1, 10, 10, 3, 9, 11, 3, 7, 7, 6, 8, 7, 4, 3, 6, 1, 4, 2, 3, 9, 7, 8, 9, 8, 5, 2, 7, 8, 5, 2, 3, 5, 8, 8, 10, 7, 5, 8, 10, 5, 8, 3, 1, 6, 6, 2, 4, 3, 11, 8, 11, 6, 3, 8, 8, 6, 6, 6, 5, 9, 7, 10, 2, 7, 8, 10, 3, 7, 8, 3, 2, 4, 7, 13, 5, 4, 4, 2, 4, 2, 2, 2, 4, 2, 4, 4, 3, 4, 2, 2, 6, 5, 4, 3, 13,], [6, 9, 4, 4, 8, 12, 3, 3, 2, 4, 3, 2, 5, 6, 3, 2, 2, 3, 7, 6, 6, 3, 7, 1, 10, 6, 3, 6, 9, 3, 7, 7, 5, 8, 7, 4, 3, 6, 2, 4, 2, 3, 10, 9, 7, 11, 7, 6, 2, 6, 6, 5, 2, 3, 5, 8, 8, 7, 9, 5, 7, 11, 4, 8, 3, 1, 8, 6, 2, 5, 3, 10, 7, 10, 6, 3, 8, 8, 6, 5, 5, 7, 9, 6, 9, 2, 9, 8, 11, 3, 6, 10, 3, 3, 5, 5, 12, 6, 5, 4, 3, 5, 3, 2, 2, 4, 2, 5, 5, 3, 3, 2, 2, 5, 4, 5, 2, 16,], ] self.verify_pscores( trees_fname="apternodus.tre", chars_fname="apternodus.chars.nexus", matrix_type=dendropy.StandardCharacterMatrix, gaps_as_missing=True, expected_scores=expected_scores, expected_per_site_scores=expected_per_site_scores) def test_pscores_with_dna_data_and_gaps_as_new_states(self): # #NEXUS # begin paup; # set warnroot = no; # exe apternodus.chars.nexus; # gett file = apternodus.tre; # set criterion = parsimony; # pset gap = newstate; # pscore; # end; expected_scores = [4703] # begin paup; # set warnroot = no; # execute pythonindae.chars.nexus; # gett file = pythonidae.mle.tre; # set crit=parsimony; # pset gap = newstate; # pscore / single = all scorefile=pythonidae.gaps-as-newstate.scores.txt; # end; expected_per_site_scores = [ [0, 6, 5, 3, 3, 3, 6, 4, 2, 3, 3, 4, 4, 4, 4, 4, 4, 3, 3, 4, 11, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 2, 3, 5, 10, 3, 6, 0, 0, 1, 3, 1, 1, 3, 1, 3, 2, 4, 4, 4, 8, 7, 7, 5, 3, 2, 2, 2, 5, 1, 0, 4, 3, 2, 2, 4, 5, 3, 6, 5, 7, 3, 10, 1, 2, 5, 10, 4, 1, 6, 2, 8, 5, 5, 5, 1, 7, 2, 3, 5, 2, 2, 1, 7, 11, 3, 4, 3, 2, 1, 1, 2, 1, 4, 10, 6, 10, 4, 10, 8, 7, 9, 11, 7, 5, 8, 3, 3, 4, 9, 7, 5, 2, 3, 3, 5, 4, 4, 3, 3, 5, 1, 5, 1, 1, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 8, 1, 4, 9, 8, 7, 9, 4, 3, 6, 8, 1, 2, 2, 7, 9, 7, 9, 5, 6, 1, 1, 1, 1, 1, 2, 4, 9, 4, 5, 3, 6, 6, 6, 5, 10, 7, 9, 4, 7, 10, 13, 8, 4, 5, 8, 9, 10, 12, 7, 9, 7, 6, 8, 8, 7, 5, 6, 6, 4, 7, 9, 8, 8, 8, 6, 7, 2, 2, 6, 5, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 3, 1, 0, 0, 0, 0, 2, 0, 0, 0, 0, 3, 0, 0, 0, 4, 0, 1, 0, 2, 0, 4, 2, 0, 1, 0, 0, 0, 7, 0, 2, 4, 1, 1, 5, 3, 0, 1, 0, 0, 0, 0, 0, 1, 0, 3, 4, 0, 0, 1, 1, 1, 6, 4, 8, 1, 0, 1, 2, 1, 10, 3, 0, 0, 0, 4, 10, 5, 3, 5, 2, 5, 4, 9, 9, 2, 4, 1, 1, 1, 7, 0, 0, 2, 0, 0, 0, 1, 5, 7, 7, 4, 2, 1, 0, 0, 0, 0, 0, 0, 1, 2, 0, 0, 0, 1, 1, 2, 2, 3, 11, 0, 1, 4, 4, 1, 2, 3, 1, 3, 2, 9, 7, 1, 3, 0, 5, 0, 0, 1, 2, 6, 2, 5, 2, 6, 1, 0, 0, 0, 8, 6, 0, 0, 0, 2, 0, 1, 1, 3, 4, 3, 1, 1, 0, 2, 1, 3, 1, 6, 0, 0, 3, 1, 1, 5, 0, 3, 1, 4, 8, 4, 6, 0, 3, 6, 3, 5, 2, 1, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 3, 0, 3, 4, 3, 3, 2, 1, 1, 0, 0, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 3, 3, 8, 4, 2, 0, 3, 5, 2, 1, 3, 2, 0, 0, 0, 0, 4, 3, 2, 3, 7, 5, 5, 0, 2, 3, 4, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 2, 0, 0, 0, 0, 0, 1, 1, 0, 0, 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0, 0, 5, 7, 1, 7, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 8, 0, 0, 0, 0, 0, 6, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 3, 3, 1, 0, 0, 0, 4, 0, 0, 0, 1, 2, 1, 0, 0, 0, 0, 0, 3, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,], ] self.verify_pscores( trees_fname="pythonidae.mle.nex", chars_fname="pythonidae.chars.nexus", matrix_type=dendropy.DnaCharacterMatrix, gaps_as_missing=False, expected_scores=expected_scores, expected_per_site_scores=expected_per_site_scores) def test_pscores_with_dna_data_and_gaps_as_missing(self): # #NEXUS # begin paup; # set warnroot = no; # exe apternodus.chars.nexus; # gett file = apternodus.tre; # set criterion = parsimony; # pset gap = newstate; # pscore; # end; expected_scores = [4271] # begin paup; # set warnroot = no; # execute pythonindae.chars.nexus; # gett file = pythonidae.mle.tre; # set crit=parsimony; # pset gap = missing; # pscore / single = all scorefile=pythonidae.gaps-as-newstate.scores.txt; # end; expected_per_site_scores = [ [0, 6, 3, 3, 3, 2, 4, 3, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 6, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 2, 8, 2, 4, 0, 0, 1, 3, 0, 0, 2, 0, 2, 1, 3, 3, 1, 2, 2, 2, 2, 2, 1, 0, 1, 5, 1, 0, 4, 3, 2, 2, 4, 2, 0, 4, 5, 7, 3, 10, 1, 2, 5, 10, 4, 1, 6, 1, 6, 3, 2, 4, 1, 7, 2, 3, 5, 2, 0, 0, 6, 10, 2, 3, 3, 2, 0, 0, 1, 0, 3, 7, 3, 7, 2, 6, 6, 4, 5, 8, 4, 2, 6, 0, 0, 1, 4, 3, 2, 0, 1, 1, 1, 1, 1, 2, 3, 4, 1, 1, 1, 0, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 7, 7, 9, 4, 1, 3, 6, 0, 2, 2, 7, 9, 7, 8, 4, 2, 0, 0, 0, 0, 0, 0, 4, 9, 4, 5, 3, 4, 3, 4, 3, 7, 5, 7, 2, 5, 7, 11, 5, 3, 4, 5, 8, 9, 11, 6, 8, 7, 6, 8, 8, 7, 5, 6, 6, 4, 6, 8, 7, 7, 6, 4, 3, 1, 1, 5, 5, 0, 0, 0, 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0, 0, 0, 1, 1, 8, 0, 0, 0, 0, 0, 6, 2, 0, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 7, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 3, 3, 1, 0, 0, 0, 4, 0, 0, 0, 1, 2, 1, 0, 0, 0, 0, 0, 3, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,] ] self.verify_pscores( trees_fname="pythonidae.mle.nex", chars_fname="pythonidae.chars.nexus", matrix_type=dendropy.DnaCharacterMatrix, gaps_as_missing=True, expected_scores=expected_scores, expected_per_site_scores=expected_per_site_scores) def verify_pscores(self, trees_fname, chars_fname, matrix_type, gaps_as_missing, expected_scores, expected_per_site_scores): taxon_namespace = dendropy.TaxonNamespace() chars = matrix_type.get( path=pathmap.char_source_path(chars_fname), schema="nexus", taxon_namespace=taxon_namespace) trees = dendropy.TreeList.get( path=pathmap.tree_source_path(trees_fname), schema="nexus", taxon_namespace=taxon_namespace) self.assertEqual(len(expected_scores), len(trees)) for tree_idx, tree in enumerate(trees): score_by_character_list = [] pscore = treescore.parsimony_score( tree, chars, gaps_as_missing=gaps_as_missing, score_by_character_list=score_by_character_list) self.assertEqual(pscore, expected_scores[tree_idx]) self.assertEqual(len(score_by_character_list), len(expected_per_site_scores[tree_idx])) for obs, exp in zip(score_by_character_list, expected_per_site_scores[tree_idx]): self.assertEqual(obs, exp) self.assertEqual(sum(score_by_character_list), pscore) # just to be sure it works without passing in `score_by_character_list`: pscore = treescore.parsimony_score( tree, chars, gaps_as_missing=gaps_as_missing) self.assertEqual(pscore, expected_scores[tree_idx]) if __name__ == "__main__": unittest.main()