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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 13);
use_ok('Bio::Tools::Run::Alignment::Probalign');
use_ok('Bio::AlignIO');
use_ok('Bio::SeqIO');
use_ok('Cwd', qw(cwd));
use_ok('POSIX');
}
END { unlink qw(cysprot.dnd cysprot1a.dnd) }
END {
unlink('probalign.log', 'probalign.out');
}
my @params = ();
my $factory = Bio::Tools::Run::Alignment::Probalign->new(@params);
my $inputfilename = test_input_file('cysprot.fa');
my $aln;
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 8);
my $version = $factory->version;
cmp_ok ($version, '>=', 3.3,"Code tested only on probalign versions > 3.3" );
$aln = $factory->align($inputfilename);
ok($aln);
is( $aln->num_sequences, 7);
my $str = Bio::SeqIO->new('-file' => $inputfilename,
'-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 PROBALIGN have different vals');
my $outfile = test_output_file();
# add some more params
@params = ('-outfile_name' => $outfile);
$factory = Bio::Tools::Run::Alignment::Probalign->new(@params);
$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 PROBALIGN 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 PROBALIGN have different vals');
}