t/ProtPars.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3 ## $Id$
   4
   5 use vars qw($DEBUG );
   6 $DEBUG = test_debug();
   7
   8 use strict;
   9 BEGIN {
  10     use Bio::Root::Test;
  11     test_begin(-tests => 11);
  12         use_ok('Bio::Tools::Run::Phylo::Phylip::ProtPars');
  13         use_ok('Bio::Tools::Run::Alignment::Clustalw');
  14 }
  15
  16 my @params = ('threshold'=>10,'jumble'=>'17,10',outgroup=>2,'idlength'=>10);
  17 my $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params);
  18 isa_ok $tree_factory,'Bio::Tools::Run::Phylo::Phylip::ProtPars';
  19
  20 SKIP: {
  21         test_skip(-requires_executable => $tree_factory,
  22                           -tests => 8);
  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
  37         my $jumble = "7,5";
  38         $tree_factory->jumble($jumble);
  39
  40         my $new_jumble= $tree_factory->jumble();
  41         is $new_jumble, "7,5", "set factory parameter";
  42
  43         my $bequiet = 1;
  44         $tree_factory->quiet($bequiet);  # Suppress protpars messages to terminal
  45
  46         my $inputfilename = test_input_file("protpars.phy");
  47         my $tree;
  48
  49         $tree = $tree_factory->create_tree($inputfilename);
  50
  51         # have to sort the since there is polytomy here.
  52         my @nodes = sort { $a->id cmp $b->id } grep { $_->id } $tree->get_nodes();
  53         is ($nodes[2]->id, 'SINFRUP002',
  54                 "creating tree by protpars");
  55
  56         $inputfilename = test_input_file("cysprot1a.fa");
  57         @params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
  58                    -verbose => -1);
  59         my  $align_factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  60
  61         SKIP: {
  62                 test_skip(-requires_executable => $align_factory,
  63                                   -tests => 4);
  64
  65                 my $aln = $align_factory->align($inputfilename);
  66
  67                 $tree = $tree_factory->create_tree($aln);
  68
  69                 @nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id } $tree->get_nodes();
  70                 is (scalar(@nodes),5,
  71                         "creating tree by protpars");
  72
  73                 # test name preservation and restoration:
  74                 @params = ('threshold'=>10,'jumble'=>'7,5',outgroup=>2,'idlength'=>10);
  75                 $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params);
  76                 $tree_factory->quiet($bequiet);  # Suppress protpars messages to terminal
  77                 $inputfilename = test_input_file("longnames.aln");
  78                 $aln = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln;
  79                 my ($aln_safe, $ref_name) =$aln->set_displayname_safe(3);
  80                 $tree = $tree_factory->create_tree($aln_safe);
  81                 @nodes = sort { $a->id cmp $b->id } $tree->get_nodes();
  82                 is (scalar(@nodes),27,
  83                         "creating tree by protpars");
  84                 is ($nodes[12]->id, 'S01',"assign serial names");
  85                 foreach my $nd (@nodes){
  86                   $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
  87                 }
  88                 is ($nodes[12]->id, 'Spar_21273',"restore original names");
  89         }
  90 }