# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use vars qw($DEBUG );
$DEBUG = test_debug();
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 11);
use_ok('Bio::Tools::Run::Phylo::Phylip::ProtPars');
use_ok('Bio::Tools::Run::Alignment::Clustalw');
}
my @params = ('threshold'=>10,'jumble'=>'17,10',outgroup=>2,'idlength'=>10);
my $tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params);
isa_ok $tree_factory,'Bio::Tools::Run::Phylo::Phylip::ProtPars';
SKIP: {
test_skip(-requires_executable => $tree_factory,
-tests => 8);
my $threshold = 5;
$tree_factory->threshold($threshold);
my $new_threshold= $tree_factory->threshold();
is $new_threshold, 5, "set factory parameter";
my $outgroup = 3;
$tree_factory->outgroup($outgroup);
my $new_outgroup= $tree_factory->outgroup();
is $new_outgroup, 3, "set factory parameter";
my $jumble = "7,5";
$tree_factory->jumble($jumble);
my $new_jumble= $tree_factory->jumble();
is $new_jumble, "7,5", "set factory parameter";
my $bequiet = 1;
$tree_factory->quiet($bequiet); # Suppress protpars messages to terminal
my $inputfilename = test_input_file("protpars.phy");
my $tree;
$tree = $tree_factory->create_tree($inputfilename);
# have to sort the since there is polytomy here.
my @nodes = sort { $a->id cmp $b->id } grep { $_->id } $tree->get_nodes();
is ($nodes[2]->id, 'SINFRUP002',
"creating tree by protpars");
$inputfilename = test_input_file("cysprot1a.fa");
@params = ('ktuple' => 2, 'matrix' => 'BLOSUM',
-verbose => -1);
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);
$tree = $tree_factory->create_tree($aln);
@nodes = sort { defined $a->id && defined $b->id && $a->id cmp $b->id } $tree->get_nodes();
is (scalar(@nodes),5, "creating tree by protpars");
# test name preservation and restoration:
@params = ('threshold'=>10,'jumble'=>'7,5',outgroup=>2,'idlength'=>10);
$tree_factory = Bio::Tools::Run::Phylo::Phylip::ProtPars->new(@params);
$tree_factory->quiet($bequiet); # Suppress protpars messages to terminal
$inputfilename = test_input_file("longnames.aln");
my $aln2 = Bio::AlignIO->new(-file=>$inputfilename, -format=>'clustalw')->next_aln;
my ($aln_safe, $ref_name) = $aln2->set_displayname_safe(3);
my $tree2 = $tree_factory->create_tree($aln_safe);
@nodes = sort { $a->id cmp $b->id } $tree2->get_nodes();
is (scalar(@nodes),27,
"creating tree by protpars");
is ($nodes[12]->id, 'S01',"assign serial names");
foreach my $nd (@nodes){
$nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
}
is ($nodes[12]->id, 'Spar_21273',"restore original names");
}
}