t/Align/TreeBuild.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7     use Bio::Root::Test;
   8
   9     test_begin(-tests => 13);
  10
  11         for my $mod ( qw(Bio::Align::DNAStatistics
  12                                          Bio::Align::ProteinStatistics
  13                                          Bio::Align::Utilities
  14                                          Bio::AlignIO
  15                                          Bio::Tree::DistanceFactory
  16                                          Bio::TreeIO) ) {
  17                 use_ok($mod);
  18     }
  19 }
  20
  21 my $debug = test_debug();
  22
  23 use Bio::Align::Utilities qw(:all);
  24
  25 my $in = Bio::AlignIO->new(-format => 'clustalw',
  26                           -file   => test_input_file('pep-266.aln'));
  27 my $aln = $in->next_aln();
  28 isa_ok($aln, 'Bio::SimpleAlign','SimpleAlign object parsed out');
  29 my $pstats = Bio::Align::ProteinStatistics->new(-verbose => $debug);
  30 my $matrix = $pstats->distance(-method => 'Kimura',
  31                                -align  => $aln);
  32 isa_ok($matrix,'Bio::Matrix::MatrixI','Protein distance matrix retrieved');
  33
  34 my $treebuilder = Bio::Tree::DistanceFactory->new(-method => 'NJ');
  35 my $tree = $treebuilder->make_tree($matrix);
  36 isa_ok($tree,'Bio::Tree::TreeI', 'Tree object gotten back');
  37
  38 my ($cn) = $tree->find_node('183.m01790');
  39
  40 # brlens checked against tree generated by PHYLIP NJ
  41 is($tree->find_node('AN2438.1')->branch_length, '0.28221','NJ calculated Branch length');
  42 is($tree->find_node('FG05298.1')->branch_length, '0.20593','NJ calculated Branch length');
  43
  44 # simple topology test - make sure these 2 are sister
  45 is($tree->find_node('YOR262W')->ancestor->id,
  46    $tree->find_node('Smik_Contig1103.1')->ancestor->id, 'Make sure two nodes are sister');
  47
  48 # TODO?
  49 # UPGMA tests
  50
  51
  52 # test the bootstrap
  53 my $replicates = &bootstrap_replicates($aln,10);
  54 is(scalar @$replicates, 10,'10 replicates formulated');