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#!/usr/local/bin/perl
#-*-Perl-*-
# ## Bioperl Test Harness Script for Modules
# #
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 12);
use_ok('Bio::AlignIO');
use_ok('Bio::Tools::Run::Alignment::Lagan');
use_ok('Bio::Root::IO');
use_ok('Bio::SeqIO');
use_ok('Bio::Seq');
use_ok('Bio::Matrix::Mlagan');
}
my $seq1 = test_input_file("lagan_dna.fa");
my $sio = Bio::SeqIO->new(-file=>$seq1,-format=>'fasta');
my $seq = $sio->next_seq;
$seq->id("first_seq");
my $seq2= Bio::Seq->new(-id=>"second_seq",-seq=>$seq->seq);
my $seq3= Bio::Seq->new(-id=>"third_seq",-seq=>$seq->seq);
my @params =
(
'order' => "\"-gs -7 -gc -2 -mt 2 -ms -1\"",
'tree' => "\"(first_seq (second_seq third_seq))\"",
'match' => 12,
'mismatch' => -8,
'gapstart' => -50,
'gapend' => -50,
'gapcont' => -2,
);
SKIP: {
my $factory = Bio::Tools::Run::Alignment::Lagan->new(@params,
-verbose => -1);
$factory->quiet(1);
isa_ok $factory,'Bio::Tools::Run::Alignment::Lagan';
test_skip(-requires_executable => $factory,
-tests => 5,
-requires_env => 'LAGAN_DIR');
my $simple_align= $factory->lagan($seq,$seq2);
isa_ok $simple_align, 'Bio::SimpleAlign';
is $simple_align->percentage_identity, 100;
my $multi = $factory->mlagan([$seq,$seq2,$seq3]);
is $multi->percentage_identity, 100;
my $matrix = Bio::Matrix::Mlagan->new(-values => [[qw(115 -161 -81 -161 0 -72)],
[qw(-161 115 -161 -81 0 -72)],
[qw(-81 -161 115 -161 0 -72)],
[qw(-161 -81 -161 115 0 -72)],
[qw(0 0 0 0 0 0)],
[qw(-72 -72 -72 -72 0 -72)]],
-gap_open => -470,
-gap_continue => -25);
is $factory->nuc_matrix($matrix), $matrix;
#*** weak test; doesn't show the supplied matrix had any effect on results...
$multi = $factory->mlagan([$seq,$seq2,$seq3]);
is $multi->percentage_identity, 100;
}