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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id$
use strict;
use vars qw($DEBUG);
$DEBUG = test_debug();
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 23);
use_ok(' Bio::Tools::Run::Alignment::MAFFT');
use_ok(' Bio::AlignIO');
use_ok(' Bio::SeqIO');
}
END { unlink qw(cysprot.dnd cysprot1a.dnd) }
my @params = (-verbose => $DEBUG,
'quiet' => 1);
my $factory = Bio::Tools::Run::Alignment::MAFFT->new(@params);
isa_ok $factory,'Bio::Tools::Run::Alignment::MAFFT';
my $inputfilename = test_input_file("cysprot.fa");
my $aln;
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 19);
$factory->executable($factory->method);
my $version = $factory->version;
ok($version);
$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 = $aln->average_percentage_identity;
cmp_ok(int($s1_perid), '>=', 42, '42 or 43 expected');
for my $method ( grep { !/rough/ } $factory->methods ) {
$factory->method($method);
$aln = $factory->align($inputfilename);
is $aln->num_sequences, 7;
my $s1_perid = $aln->average_percentage_identity;
ok($s1_perid);
}
SKIP: {
skip("Tests require version 6 of MAFFT", 6) unless $factory->_version6;
$factory->localpair(1);
$aln = $factory->align( $inputfilename );
is $aln->num_sequences, 7;
$s1_perid = $aln->average_percentage_identity;
ok($s1_perid);
$factory->globalpair(1);
throws_ok { $aln = $factory->align( $inputfilename ) }
qr/You can't specify more than one of/,
'More than one alignment method throws';
my @extra_params = qw/ localpair 1 maxiterate 10000 /;
$factory = Bio::Tools::Run::Alignment::MAFFT->new(@params, @extra_params);
isa_ok $factory,'Bio::Tools::Run::Alignment::MAFFT';
$aln = $factory->align( $inputfilename );
is $aln->num_sequences, 7;
$s1_perid = $aln->average_percentage_identity;
ok($s1_perid);
}
}
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