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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id$
use strict;
use vars qw($DEBUG);
$DEBUG = test_debug() || -1;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 14);
use_ok('Bio::Tools::Run::Phylo::Phylip::ProtDist');
use_ok('Bio::Tools::Run::Alignment::Clustalw');
}
my $verbose = $DEBUG;
my @params = (
'idlength' =>30,
'model' =>'pam',
'gencode' =>'U',
'category' =>'H',
'probchange'=>'0.4',
'trans' =>'5',
'freq' =>'0.25,0.5,0.125,0.125');
my $dist_factory = Bio::Tools::Run::Phylo::Phylip::ProtDist->new(@params);
SKIP: {
test_skip(-requires_executable => $dist_factory,
-tests => 12);
isa_ok $dist_factory,'Bio::Tools::Run::Phylo::Phylip::ProtDist';
my $model = 'KIMURA';
$dist_factory->model($model);
my $new_model= $dist_factory->model();
is $new_model , 'KIMURA', "set factory parameter";
my $gencode = 'M';
$dist_factory->gencode($gencode);
my $new_gencode= $dist_factory->gencode();
is $new_gencode, 'M', "set factory parameter";
my $category= "H";
$dist_factory->category($category);
my $new_category= $dist_factory->category();
is $new_category, "H", "set factory parameter";
my $probchange= 0.4;
$dist_factory->probchange($probchange);
my $new_probchange= $dist_factory->probchange();
is $new_probchange, 0.4, "set factory parameter";
my $trans= 5;
$dist_factory->trans($trans);
my $new_trans= $dist_factory->trans();
is $new_trans, 5, "set factory parameter";
my $freq= "0.25,0.5,0.125,0.125";
$dist_factory->freq($freq);
my $new_freq= $dist_factory->freq();
is $new_freq, "0.25,0.5,0.125,0.125", "set factory parameter";
my $bequiet = 1;
$dist_factory->quiet($bequiet); # Suppress protpars messages to terminal
my $inputfilename = test_input_file("protpars.phy");
my $matrix;
$dist_factory->verbose($verbose);
($matrix) = $dist_factory->create_distance_matrix($inputfilename);
is(sprintf("%.3f", $matrix->get_entry('ENSP000003','SINFRUP001')),0.277);
$inputfilename = test_input_file("cysprot.fa");
@params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
-verbose => $verbose);
my $align_factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
SKIP: {
test_skip(-requires_executable => $align_factory,
-tests => 4);
my $aln = $align_factory->align($inputfilename);
($matrix) = $dist_factory->create_distance_matrix($aln);
is (int($matrix->get_entry('ALEU_HORVU','ALEU_HORVU')),0,
"creating distance matrix");
ok(sprintf("%.2f",$matrix->get_entry('CATL_HUMAN','CYS1_DICDI'),'1.30', "creating distance matrix"));
# Test name preservation and restoration:
$inputfilename = test_input_file("longnames.aln");
$aln = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln;
my ($aln_safe, $ref_name) =$aln->set_displayname_safe(3);
($matrix) = $dist_factory->create_distance_matrix($aln_safe);
is (int($matrix->get_entry('S03','S03')),0, "failed creating matrix on safe names");
ok(sprintf("%.4f",$matrix->get_entry('S01','S02'),'0.0205', "failed creating distance matrix"));
}
}
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