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 = $ENV{'BIOPERLDEBUG'} || -1;
   8
   9 BEGIN {
  10     eval { require Test; };
  11     if( $@ ) {
  12         use lib 't';
  13     }
  14     use Test;
  15     use vars qw($NTESTS);
  16     $NTESTS = 11;
  17     plan tests => $NTESTS;
  18 }
  19
  20 use Bio::Tools::Run::Phylo::Phylip::ProtDist;
  21 use Bio::Tools::Run::Alignment::Clustalw;
  22
  23 END {
  24     for ( $Test::ntest..$NTESTS ) {
  25         skip("ProtDist not found. Skipping.",1);
  26     }
  27 }
  28
  29 ok(1);
  30 my $verbose = $DEBUG;
  31 my @params = (
  32               'idlength'  =>30,
  33               'model'     =>'pam',
  34               'gencode'   =>'U',
  35               'category'  =>'H',
  36               'probchange'=>'0.4',
  37               'trans'     =>'5',
  38               'freq'      =>'0.25,0.5,0.125,0.125');
  39
  40 my $dist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
  41 unless($dist_factory->executable){
  42     warn("Protdist program not found. Skipping tests $Test::ntest to $NTESTS.\n");
  43     exit 0;
  44 }
  45
  46 ok $dist_factory->isa('Bio::Tools::Run::Phylo::Phylip::ProtDist');
  47
  48 my $model = 'KIMURA';
  49 $dist_factory->model($model);
  50
  51 my $new_model= $dist_factory->model();
  52 ok $new_model , 'KIMURA', " couldn't set factory parameter";
  53
  54 my $gencode = 'M';
  55 $dist_factory->gencode($gencode);
  56
  57 my $new_gencode= $dist_factory->gencode();
  58 ok $new_gencode, 'M', " couldn't set factory parameter";
  59
  60
  61 my $category= "H";
  62 $dist_factory->category($category);
  63
  64 my $new_category= $dist_factory->category();
  65 ok $new_category, "H", " couldn't set factory parameter";
  66
  67 my $probchange= 0.4;
  68 $dist_factory->probchange($probchange);
  69
  70 my $new_probchange= $dist_factory->probchange();
  71 ok $new_probchange, 0.4, " couldn't set factory parameter";
  72
  73 my $trans= 5;
  74 $dist_factory->trans($trans);
  75
  76 my $new_trans= $dist_factory->trans();
  77 ok $new_trans, 5, " couldn't set factory parameter";
  78
  79 my $freq= "0.25,0.5,0.125,0.125";
  80 $dist_factory->freq($freq);
  81
  82 my $new_freq= $dist_factory->freq();
  83 ok $new_freq, "0.25,0.5,0.125,0.125", " couldn't set factory parameter";
  84
  85 my $bequiet = 1;
  86 $dist_factory->quiet($bequiet);  # Suppress protpars messages to terminal
  87
  88 my $inputfilename = Bio::Root::IO->catfile("t","data","protpars.phy");
  89 my $matrix;
  90 my $protdist_present = $dist_factory->executable();
  91 unless ($protdist_present) {
  92     warn("protdist program not found. Skipping tests $Test::ntest to $NTESTS.\n") if($DEBUG);
  93     exit 0;
  94 }
  95 $dist_factory->verbose($verbose);
  96 ($matrix) = $dist_factory->create_distance_matrix($inputfilename);
  97
  98 ok(sprintf("%.3f", $matrix->get_entry('ENSP000003','SINFRUP001')),0.277);
  99
 100 $inputfilename = Bio::Root::IO->catfile("t","data","cysprot.fa");
 101 @params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
 102            -verbose => $verbose);
 103 my  $align_factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
 104
 105 exit(0) unless $align_factory->executable();
 106
 107 my $aln = $align_factory->align($inputfilename);
 108 ($matrix) = $dist_factory->create_distance_matrix($aln);
 109
 110 ok (int($matrix->get_entry('ALEU_HORVU','ALEU_HORVU')),0,
 111     "failed creating distance matrix");
 112 ok(sprintf("%.2f",$matrix->get_entry('CATL_HUMAN','CYS1_DICDI'),'1.30', "failed creating distance matrix"));