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# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 10,
-requires_module =>'IO::String');
use_ok('Bio::Tools::Run::Phylo::Hyphy::SLAC');
use_ok('Bio::Tools::Run::Phylo::Hyphy::FEL');
use_ok('Bio::Tools::Run::Phylo::Hyphy::REL');
use_ok('Bio::Tools::Run::Phylo::Hyphy::Modeltest');
use_ok('Bio::Tools::Run::Phylo::Hyphy::BatchFile');
}
SKIP: {
my $rel = Bio::Tools::Run::Phylo::Hyphy::REL->new();
test_skip(-requires_executable => $rel,
-tests => 5);
my $alignio = Bio::AlignIO->new(-format => 'fasta',
-file => 't/data/hyphy1.fasta');
my $treeio = Bio::TreeIO->new(-format => 'newick',
-file => 't/data/hyphy1.tree');
my $aln = $alignio->next_aln;
my $tree = $treeio->next_tree;
my $debug = test_debug();
my ($rc,$results);
$rel->alignment($aln);
$rel->tree($tree);
($rc,$results) = $rel->run();
if (($rc == 0) && ($debug == 1)){
warn("ERROR in REL module $rc:" . $rel->error_string() . "\n");
}
ok ($rc != 0, "REL module");
my $fel = Bio::Tools::Run::Phylo::Hyphy::FEL->new();
$fel->alignment($aln);
$fel->tree($tree);
($rc,$results) = $fel->run();
if (($rc == 0) && ($debug == 1)){
warn("ERROR in FEL module $rc:" . $fel->error_string() . "\n");
}
ok (defined($results->{'LRT'}), "FEL module");
my $modeltest = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
$modeltest->alignment($aln);
$modeltest->tree($tree);
($rc,$results) = $modeltest->run();
if (($rc == 0) && ($debug == 1)){
warn("ERROR in Modeltest module $rc:" . $modeltest->error_string() . "\n");
}
ok (defined($results->{'AIC'}), "Modeltest module");
my $bf_exec = Bio::Tools::Run::Phylo::Hyphy::BatchFile->new(
-params => {'bf' => "ModelTest.bf",
'order' => [$aln, $tree, '4', 'AIC Test', ""]}
);
$bf_exec->alignment($aln);
$bf_exec->tree($tree);
my ($tfh, $t) = $bf_exec->io->tempfile;
$bf_exec->set_parameter(5, $t);
$bf_exec->version();
($rc,$results) = $bf_exec->run();
if (($rc == 0) && ($debug == 1)){
warn("ERROR in Batchfile module $rc:" . $bf_exec->error_string() . "\n");
}
ok ($rc != 0, "Batchfile module");
my $slac = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();
$slac->alignment($aln);
$slac->tree($tree);
($rc,$results) = $slac->run();
if (($rc == 0) && ($debug == 1)){
warn("ERROR in SLAC module $rc:" . $slac->error_string() . "\n");
}
ok (defined($results->{'Observed NS Changes'}), "SLAC module");
}