t/ProtDist.t

   1 # -*-Perl-*-
   2 ## Bioperl Test Harness Script for Modules
   3 #
   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 }
  14
  15 my $verbose = $DEBUG;
  16 my @params = (
  17               'idlength'  =>30,
  18               'model'     =>'pam',
  19               'gencode'   =>'U',
  20               'category'  =>'H',
  21               'probchange'=>'0.4',
  22               'trans'     =>'5',
  23               'freq'      =>'0.25,0.5,0.125,0.125');
  24
  25 my $dist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
  26
  27 SKIP: {
  28         test_skip(-requires_executable => $dist_factory,
  29               -requires_module => 'Bio::Tools::Run::Alignment::Clustalw',
  30                   -tests => 13);
  31
  32         use_ok('Bio::Tools::Run::Alignment::Clustalw');
  33         isa_ok $dist_factory,'Bio::Tools::Run::Phylo::Phylip::ProtDist';
  34
  35         my $model = 'KIMURA';
  36         $dist_factory->model($model);
  37
  38         my $new_model= $dist_factory->model();
  39         is $new_model , 'KIMURA', "set factory parameter";
  40
  41         my $gencode = 'M';
  42         $dist_factory->gencode($gencode);
  43
  44         my $new_gencode= $dist_factory->gencode();
  45         is $new_gencode, 'M', "set factory parameter";
  46
  47         my $category= "H";
  48         $dist_factory->category($category);
  49
  50         my $new_category= $dist_factory->category();
  51         is $new_category, "H", "set factory parameter";
  52
  53         my $probchange= 0.4;
  54         $dist_factory->probchange($probchange);
  55
  56         my $new_probchange= $dist_factory->probchange();
  57         is $new_probchange, 0.4, "set factory parameter";
  58
  59         my $trans= 5;
  60         $dist_factory->trans($trans);
  61
  62         my $new_trans= $dist_factory->trans();
  63         is $new_trans, 5, "set factory parameter";
  64
  65         my $freq= "0.25,0.5,0.125,0.125";
  66         $dist_factory->freq($freq);
  67
  68         my $new_freq= $dist_factory->freq();
  69         is $new_freq, "0.25,0.5,0.125,0.125", "set factory parameter";
  70
  71         my $bequiet = 1;
  72         $dist_factory->quiet($bequiet);  # Suppress protpars messages to terminal
  73
  74         my $inputfilename = test_input_file("protpars.phy");
  75         my $matrix;
  76
  77         $dist_factory->verbose($verbose);
  78         ($matrix) = $dist_factory->create_distance_matrix($inputfilename);
  79
  80         is(sprintf("%.3f", $matrix->get_entry('ENSP000003','SINFRUP001')),0.277);
  81
  82         $inputfilename = test_input_file("cysprot.fa");
  83         @params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
  84                    -verbose => $verbose);
  85         my  $align_factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
  86
  87         SKIP: {
  88                 test_skip(-requires_executable => $align_factory,
  89                                   -tests => 4);
  90
  91                 my $aln = $align_factory->align($inputfilename);
  92                 ($matrix) = $dist_factory->create_distance_matrix($aln);
  93
  94                 is (int($matrix->get_entry('ALEU_HORVU','ALEU_HORVU')),0,
  95                         "creating distance matrix");
  96                 ok(sprintf("%.2f",$matrix->get_entry('CATL_HUMAN','CYS1_DICDI'),'1.30', "creating distance matrix"));
  97
  98                 # Test name preservation and restoration:
  99                 $inputfilename = test_input_file("longnames.aln");
 100                 $aln = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln;
 101                 my ($aln_safe, $ref_name) =$aln->set_displayname_safe(3);
 102                 ($matrix) = $dist_factory->create_distance_matrix($aln_safe);
 103                 is (int($matrix->get_entry('S03','S03')),0, "failed creating matrix on safe names");
 104                 ok(sprintf("%.4f",$matrix->get_entry('S01','S02'),'0.0205', "failed creating distance matrix"));
 105         }
 106 }
 107