t/LVB.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3
   4 use vars qw($DEBUG );
   5 $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;
   6
   7 use strict;
   8 BEGIN {
   9     eval { require Test; };
  10     if( $@ ) {
  11         use lib 't';
  12     }
  13     use Test;
  14     use vars qw($NTESTS);
  15     $NTESTS = 20;
  16     plan tests => $NTESTS;
  17 }
  18
  19 use Bio::Tools::Run::Phylo::LVB;
  20 use Bio::AlignIO;
  21 END {
  22     for ( $Test::ntest..$NTESTS ) {
  23         skip("LVB not found. Skipping.",1);
  24     }
  25 }
  26
  27 ok(1);
  28 my $tree_factory = Bio::Tools::Run::Phylo::LVB->new();
  29 ok $tree_factory->isa('Bio::Tools::Run::Phylo::LVB');
  30
  31 unless($tree_factory->executable){
  32     warn("LVB program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  33     exit 0;
  34 }
  35
  36 my $default_format = "interleaved";
  37 my $format = $tree_factory->format;
  38 ok $format, $default_format, "default is wrong for format parameter";
  39 $format = "sequential";
  40 $tree_factory->format($format);
  41 my $new_format = $tree_factory->format();
  42 ok $new_format, $format, "couldn't set format parameter";
  43 $format = "interleaved";
  44 $tree_factory->format($format);
  45 $new_format = $tree_factory->format();
  46 ok $new_format, $format, "couldn't reset format parameter";
  47
  48 my $default_gaps = "unknown";
  49 my $gaps = $tree_factory->gaps;
  50 ok $gaps, $default_gaps, "default is wrong for gaps parameter";
  51 $gaps = "fifthstate";
  52 $tree_factory->gaps($gaps);
  53 my $new_gaps = $tree_factory->gaps();
  54 ok $new_gaps, $gaps, "couldn't set gaps parameter";
  55 $gaps = "unknown";
  56 $tree_factory->gaps($gaps);
  57 $new_gaps = $tree_factory->gaps();
  58 ok $new_gaps, $gaps, "couldn't reset gaps parameter";
  59
  60 my $default_seed = "";
  61 my $seed = $tree_factory->seed;
  62 ok $seed, $default_seed, "default is wrong for seed parameter";
  63 $seed = "96901";
  64 $tree_factory->seed($seed);
  65 my $new_seed = $tree_factory->seed();
  66 ok $new_seed, $seed, "couldn't set seed parameter";
  67
  68 my $default_duration = "slow";
  69 my $duration = $tree_factory->duration;
  70 ok $duration, $default_duration, "default is wrong for duration parameter";
  71 $duration = "fast";
  72 $tree_factory->duration($duration);
  73 my $new_duration = $tree_factory->duration();
  74 ok $new_duration, $duration, "couldn't set duration parameter";
  75 $duration = "slow";
  76 $tree_factory->duration($duration);
  77 $new_duration = $tree_factory->duration();
  78 ok $new_duration, $duration, "couldn't reset duration parameter";
  79
  80 my $default_bootstraps = 0;
  81 my $bootstraps = $tree_factory->bootstraps;
  82 ok $bootstraps, $default_bootstraps, "default is wrong for bootstraps parameter";
  83 $bootstraps = "10000";
  84 $tree_factory->bootstraps($bootstraps);
  85 my $new_bootstraps = $tree_factory->bootstraps();
  86 ok $new_bootstraps, $bootstraps, "couldn't set bootstraps parameter";
  87 $bootstraps = 0;
  88 $tree_factory->bootstraps($bootstraps);
  89 $new_bootstraps = $tree_factory->bootstraps();
  90 $new_bootstraps = $tree_factory->bootstraps();
  91 ok $new_bootstraps, $bootstraps, "couldn't reset seed parameter";
  92
  93 my $bequiet = 1;
  94 $tree_factory->quiet($bequiet);  # Suppress LVB messages to terminal
  95
  96 my @trees;
  97
  98 # TEST 17
  99 $tree_factory->format("sequential");
 100 my $inputfilename = Bio::Root::IO->catfile("t","data","lvb_sequential.phy");
 101 @trees = $tree_factory->create_tree($inputfilename);
 102 ok scalar(@trees), 3, "create_tree failed to create array of trees from file";
 103
 104 # TEST 18
 105 $inputfilename = Bio::Root::IO->catfile("t","data","lvb.fa");
 106 my $align_in = Bio::AlignIO->new(-file => $inputfilename, -format => "fasta");
 107 my $align_obj = $align_in->next_aln;
 108 @trees = $tree_factory->run($align_obj);
 109 ok scalar(@trees), 3, "run failed to create array of trees from object";
 110
 111 $tree_factory->gaps("fifthstate");
 112 @trees = $tree_factory->run($align_obj);
 113 ok scalar(@trees), 1, "run failed to create tree with fifthstate on";
 114
 115 $tree_factory->bootstraps(7);
 116 @trees = $tree_factory->run($align_obj);
 117 my $enough_trees = "no";
 118 $enough_trees = "yes" if scalar(@trees) >= 7;
 119 ok $enough_trees, "yes", "run failed to create enough bootstrap trees";