t/Njtree.t

   1 # This is -*-Perl-*- code
   2 ## Bioperl Test Harness Script for Modules
   3 ##
   4
   5 # Before `make install' is performed this script should be runnable with
   6 # `make test'. After `make install' it should work as `perl test.t'
   7
   8 use strict;
   9
  10 BEGIN {
  11     use Bio::Root::Test;
  12     test_begin(-tests => 6,
  13                            -requires_module => 'IO::String');
  14         use_ok('Bio::Root::IO');
  15         use_ok('Bio::Tools::Run::Phylo::Njtree::Best');
  16         use_ok('Bio::AlignIO');
  17         use_ok('Bio::TreeIO');
  18 }
  19
  20 ok my $njtree_best = Bio::Tools::Run::Phylo::Njtree::Best->new();
  21
  22 SKIP: {
  23         test_skip(-requires_executable => $njtree_best,
  24                           -tests => 1);
  25
  26         my $alignio = Bio::AlignIO->new(-format => 'fasta',
  27                                                                         -file   => test_input_file('njtree_aln2.nucl.mfa'));
  28         my $aln = $alignio->next_aln;
  29
  30         my $treeio = Bio::TreeIO->new(
  31                 -format => 'nhx',
  32                 -file => test_input_file('species_tree_njtree.nh'));
  33         my $tree = $treeio->next_tree;
  34
  35         $njtree_best->alignment($aln);
  36         $njtree_best->tree($tree);
  37         $njtree_best->check_names();
  38
  39         my ($rc,$nhx_tree) = $njtree_best->run();
  40         print $njtree_best->error_string, "\n";
  41         ok $nhx_tree;
  42
  43         #*** where are the tests?!
  44 }