# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 16);
use_ok('Bio::Tools::Run::Alignment::Muscle');
use_ok('Bio::AlignIO');
use_ok('Bio::SeqIO');
use_ok('Bio::Root::IO');
use_ok('POSIX');
}
END {
unlink('muscle.log', 'muscle.out');
unlink qw(cysprot.dnd cysprot1a.dnd);
}
my @params = ('quiet' => 1);
my $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);
is($factory->quiet, 1);
my $inputfilename = test_input_file("cysprot.fa");
my $aln;
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 10);
my $version = $factory->version;
unless ($version >= 3.6) {
skip("Only muscle version 3.6 or higher is supported by these tests. Skipping tests", 7);
exit(0);
}
cmp_ok ($version, '>=', 3.6, "Code tested only on muscle versions > 3.6" );
$aln = $factory->align($inputfilename);
ok($aln);
is( $aln->num_sequences, 7);
my $str = Bio::SeqIO->new('-file' =>
test_input_file("cysprot.fa"),
'-format' => 'Fasta');
my @seq_array =();
while ( my $seq = $str->next_seq() ) {
push (@seq_array, $seq) ;
}
my $seq_array_ref = \@seq_array;
$aln = $factory->align($seq_array_ref);
is $aln->num_sequences, 7;
my $s1_perid = POSIX::ceil($aln->average_percentage_identity);
is($s1_perid == 43 || $s1_perid == 44, 1,
'diff versions of MUSCLE have different vals');
my $logfile = test_output_file();
my $outfile = test_output_file();
# add some more params
@params = ('quiet' => 1,
'-outfile_name' => $outfile,
'diags' => 1,
'stable' => 1,
'maxmb' => 50,
'maxhours' => 1,
'maxiters' => 20,
'log' => $logfile,
);
$factory = Bio::Tools::Run::Alignment::Muscle->new(@params);
is($factory->log, $logfile,'log file');
$aln = $factory->align($seq_array_ref);
is $aln->num_sequences, 7;
$s1_perid = POSIX::ceil($aln->average_percentage_identity);
is($s1_perid == 43 || $s1_perid == 44, 1,
'diff versions of MUSCLE have different vals');
$inputfilename = test_input_file("cysprot1a.fa");
$aln = $factory->align($inputfilename);
is $aln->num_sequences, 3;
$s1_perid = POSIX::ceil($aln->average_percentage_identity);
is($s1_perid == 41 || $s1_perid == 42, 1,
'diff versions of MUSCLE have different vals');
}