t/ProtDist.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3 ## $Id$
   4
   5 use strict;
   6 use vars qw($DEBUG);
   7 $DEBUG = test_debug() || -1;
   8
   9 BEGIN {
  10     use Bio::Root::Test;
  11     test_begin(-tests => 14);
  12         use_ok('Bio::Tools::Run::Phylo::Phylip::ProtDist');
  13         use_ok('Bio::Tools::Run::Alignment::Clustalw');
  14 }
  15
  16 my $verbose = $DEBUG;
  17 my @params = (
  18               'idlength'  =>30,
  19               'model'     =>'pam',
  20               'gencode'   =>'U',
  21               'category'  =>'H',
  22               'probchange'=>'0.4',
  23               'trans'     =>'5',
  24               'freq'      =>'0.25,0.5,0.125,0.125');
  25
  26 my $dist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
  27
  28 SKIP: {
  29         test_skip(-requires_executable => $dist_factory,
  30                   -tests => 12);
  31
  32         isa_ok $dist_factory,'Bio::Tools::Run::Phylo::Phylip::ProtDist';
  33
  34         my $model = 'KIMURA';
  35         $dist_factory->model($model);
  36
  37         my $new_model= $dist_factory->model();
  38         is $new_model , 'KIMURA', "set factory parameter";
  39
  40         my $gencode = 'M';
  41         $dist_factory->gencode($gencode);
  42
  43         my $new_gencode= $dist_factory->gencode();
  44         is $new_gencode, 'M', "set factory parameter";
  45
  46         my $category= "H";
  47         $dist_factory->category($category);
  48
  49         my $new_category= $dist_factory->category();
  50         is $new_category, "H", "set factory parameter";
  51
  52         my $probchange= 0.4;
  53         $dist_factory->probchange($probchange);
  54
  55         my $new_probchange= $dist_factory->probchange();
  56         is $new_probchange, 0.4, "set factory parameter";
  57
  58         my $trans= 5;
  59         $dist_factory->trans($trans);
  60
  61         my $new_trans= $dist_factory->trans();
  62         is $new_trans, 5, "set factory parameter";
  63
  64         my $freq= "0.25,0.5,0.125,0.125";
  65         $dist_factory->freq($freq);
  66
  67         my $new_freq= $dist_factory->freq();
  68         is $new_freq, "0.25,0.5,0.125,0.125", "set factory parameter";
  69
  70         my $bequiet = 1;
  71         $dist_factory->quiet($bequiet);  # Suppress protpars messages to terminal
  72
  73         my $inputfilename = test_input_file("protpars.phy");
  74         my $matrix;
  75
  76         $dist_factory->verbose($verbose);
  77         ($matrix) = $dist_factory->create_distance_matrix($inputfilename);
  78
  79         is(sprintf("%.3f", $matrix->get_entry('ENSP000003','SINFRUP001')),0.277);
  80
  81         $inputfilename = test_input_file("cysprot.fa");
  82         @params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
  83                    -verbose => $verbose);
  84         my  $align_factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  85
  86         SKIP: {
  87                 test_skip(-requires_executable => $align_factory,
  88                                   -tests => 4);
  89
  90                 my $aln = $align_factory->align($inputfilename);
  91                 ($matrix) = $dist_factory->create_distance_matrix($aln);
  92
  93                 is (int($matrix->get_entry('ALEU_HORVU','ALEU_HORVU')),0,
  94                         "creating distance matrix");
  95                 ok(sprintf("%.2f",$matrix->get_entry('CATL_HUMAN','CYS1_DICDI'),'1.30', "creating distance matrix"));
  96
  97                 # Test name preservation and restoration:
  98                 $inputfilename = test_input_file("longnames.aln");
  99                 $aln = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln;
 100                 my ($aln_safe, $ref_name) =$aln->set_displayname_safe(3);
 101                 ($matrix) = $dist_factory->create_distance_matrix($aln_safe);
 102                 is (int($matrix->get_entry('S03','S03')),0, "failed creating matrix on safe names");
 103                 ok(sprintf("%.4f",$matrix->get_entry('S01','S02'),'0.0205', "failed creating distance matrix"));
 104         }
 105 }
 106