t/ProtPars.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3
   4 use vars qw($DEBUG );
   5 $DEBUG = test_debug();
   6
   7 use strict;
   8 BEGIN {
   9     use Bio::Root::Test;
  10     test_begin(-tests => 11);
  11         use_ok('Bio::Tools::Run::Phylo::Phylip::ProtPars');
  12 }
  13
  14 my @params = ('threshold'=>10,'jumble'=>'17,10',outgroup=>2,'idlength'=>10);
  15 my $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params);
  16 isa_ok $tree_factory,'Bio::Tools::Run::Phylo::Phylip::ProtPars';
  17
  18 SKIP: {
  19         test_skip(-requires_executable => $tree_factory,
  20               -requires_module => 'Bio::Tools::Run::Alignment::Clustalw',
  21                           -tests => 9);
  22         use_ok('Bio::Tools::Run::Alignment::Clustalw');
  23
  24         my $threshold = 5;
  25         $tree_factory->threshold($threshold);
  26
  27         my $new_threshold= $tree_factory->threshold();
  28         is $new_threshold, 5, "set factory parameter";
  29
  30         my $outgroup = 3;
  31         $tree_factory->outgroup($outgroup);
  32
  33         my $new_outgroup= $tree_factory->outgroup();
  34         is $new_outgroup, 3, "set factory parameter";
  35
  36         my $jumble = "7,5";
  37         $tree_factory->jumble($jumble);
  38
  39         my $new_jumble= $tree_factory->jumble();
  40         is $new_jumble, "7,5", "set factory parameter";
  41
  42         my $bequiet = 1;
  43         $tree_factory->quiet($bequiet);  # Suppress protpars messages to terminal
  44
  45         my $inputfilename = test_input_file("protpars.phy");
  46         my $tree;
  47
  48         $tree = $tree_factory->create_tree($inputfilename);
  49
  50         # have to sort the since there is polytomy here.
  51         my @nodes = sort { $a->id cmp $b->id } grep { $_->id } $tree->get_nodes();
  52         is ($nodes[2]->id, 'SINFRUP002',
  53                 "creating tree by protpars");
  54
  55         $inputfilename = test_input_file("cysprot1a.fa");
  56         @params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
  57                    -verbose => -1);
  58         my  $align_factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  59
  60         SKIP: {
  61                 test_skip(-requires_executable => $align_factory,
  62                                   -tests => 4);
  63
  64                 my $aln = $align_factory->align($inputfilename);
  65
  66                 $tree = $tree_factory->create_tree($aln);
  67
  68                 @nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id } $tree->get_nodes();
  69                 is (scalar(@nodes),5, "creating tree by protpars");
  70
  71                 # test name preservation and restoration:
  72                 @params = ('threshold'=>10,'jumble'=>'7,5',outgroup=>2,'idlength'=>10);
  73                 $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params);
  74                 $tree_factory->quiet($bequiet);  # Suppress protpars messages to terminal
  75                 $inputfilename = test_input_file("longnames.aln");
  76                 my $aln2 = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln;
  77                 my ($aln_safe, $ref_name) = $aln2->set_displayname_safe(3);
  78                 my $tree2 = $tree_factory->create_tree($aln_safe);
  79                 @nodes = sort { $a->id cmp $b->id } $tree2->get_nodes();
  80                 is (scalar(@nodes),27,
  81                         "creating tree by protpars");
  82                 is ($nodes[12]->id, 'S01',"assign serial names");
  83                 foreach my $nd (@nodes){
  84                   $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
  85                 }
  86                 is ($nodes[12]->id, 'Spar_21273',"restore original names");
  87         }
  88 }