# This is -*-Perl-*- code
## Bioperl Test Harness Script for Modules
##
# $Id$
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use vars qw($NUMTESTS);
my $error;
my $serror;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 10,
-requires_module => 'IO::String');
use_ok('Bio::Tools::Phylo::Molphy'); # PAML parser
use_ok('Bio::Tools::Run::Phylo::Molphy::ProtML');
use_ok('Bio::AlignIO');
}
my $verbose = test_debug();
END { unlink('protml.eps'); }
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my %args = ( 'models' => 'jtt',
'search' => 'quick',
"other" => [ '-information', '-w']);
my $protml = Bio::Tools::Run::Phylo::Molphy::ProtML->new(-verbose => $verbose,
-flags => \%args);
SKIP: {
test_skip(-requires_executable => $protml,
-tests => 7);
my $in = Bio::AlignIO->new(-format => 'clustalw',
-file => test_input_file('cel-cbr-fam.aln'));
my $aln = $in->next_aln;
$protml->alignment($aln);
my ($rc,$results) = $protml->run();
is($rc,1);
my $r = $results->next_result;
ok($r);
my @trees;
while( my $t = $r->next_tree ) {
push @trees, $t;
}
is(@trees,1);
is($r->model, 'JTT');
is($r->search_space,50);
is($trees[0]->score, -453.1);
ok($protml->error_string !~ /Error/); # we don't expect any errors;
}