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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 9);
use_ok('Bio::Tools::Run::Alignment::Pal2Nal');
}
# setup input files etc
my $nucleotide_filename = test_input_file('pal2nal.nuc');
my $protein_alignfilename = test_input_file('pal2nal.aln');
my $mxlib = test_input_file('transfac.dat');
my $factory = Bio::Tools::Run::Alignment::Pal2Nal->new();
isa_ok($factory, 'Bio::Tools::Run::Alignment::Pal2Nal');
# test default factory values
is ($factory->program_dir, $ENV{'PAL2NALDIR'}, 'program_dir returned correct default');
is ($factory->program_name(), 'pal2nal.pl', 'Correct exe default name');
# test the program itself
SKIP: {
test_skip(-requires_executable => $factory,
-tests => 5);
# Run Pal2Nal with a protein alignment file and a multi-fasta nucleotide
# file
ok my $aln1 = $factory->run($protein_alignfilename, $nucleotide_filename);
# or with Bioperl objects
use_ok('Bio::AlignIO');
use_ok('Bio::SeqIO');
my $ai = Bio::AlignIO->new(-file => $protein_alignfilename);
my $protein_bio_simplalign = $ai->next_aln;
my $si = Bio::SeqIO->new(-file => $nucleotide_filename, -format => 'fasta');
my $nucleotide_bio_seq1 = $si->next_seq;
my $nucleotide_bio_seq2 = $si->next_seq;
ok my $aln2 = $factory->run($protein_bio_simplalign,
[$nucleotide_bio_seq1, $nucleotide_bio_seq2]);
is_deeply($aln1, $aln2);
}