~ubuntu-branches/ubuntu/precise/bioperl/precise

# -*-Perl-*- Test Harness script for Bioperl

# $Id: po.t 14971 2008-10-28 16:08:52Z cjfields $

use strict;

BEGIN {

	use lib '.';

    use Bio::Root::Test;

    test_begin(-tests => 11);

	use_ok('Bio::AlignIO::po');

}

my $DEBUG = test_debug();

my ($str,$aln,$strout,$status);

# POA

# just skip on perl 5.6.0 and earlier as it causes a crash on 

# default perl with OS X 10.2

# fink perl 5.6.0 does not seem to have the problem

# can't figure out what it is so just skip for now

SKIP: {

	skip("skipping due to bug in perl 5.6.0 that comes with OS X 10.2", 10) unless ($^O ne 'darwin' || $] > 5.006);

	$str = Bio::AlignIO->new(

			  -file   => test_input_file('testaln.po'),

			  -format => 'po',

			  );

	isa_ok($str, 'Bio::AlignIO');

	$aln = $str->next_aln();

	isa_ok($aln,'Bio::Align::AlignI');

	is $aln->num_sequences, 6;

	# output is? i.e. does conversion from clustalw to po give the same alignment?

	$str = Bio::AlignIO->new(

		  '-file'   => test_input_file('testaln.aln'),

		  '-format' => 'clustalw');

	isa_ok($str,'Bio::AlignIO');

	$aln = $str->next_aln();

	isa_ok($aln,'Bio::Align::AlignI');

	$strout = Bio::AlignIO->new(

		 '-file'   => ">" . test_output_file(),

		 '-format' => 'po');

	$status = $strout->write_aln($aln);

	is $status, 1, "po output test";

	$str = Bio::AlignIO->new(

		 '-file'   => test_input_file('testaln.po'),

		 '-format' => 'po');

	isa_ok($str,'Bio::AlignIO');

	my $aln2 = $str->next_aln();

	isa_ok($aln2,'Bio::Align::AlignI');

	is $aln2->num_sequences, $aln->num_sequences;

	is $aln2->length, $aln->length;

}