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# -*-Perl-*- Test Harness script for Bioperl
# $Id: xmfa.t 14971 2008-10-28 16:08:52Z cjfields $
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 30);
use_ok('Bio::AlignIO::xmfa');
}
my $DEBUG = test_debug(); # foo
my ($str,$aln,$strout,$status);
# XMFA
$str = Bio::AlignIO->new(
-file => test_input_file("testaln.xmfa"),
-format => 'xmfa');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
# test seqs
my @test_data = (
# 1:1-598 + chrY
[ 'chrY/1-598', 1, 598, 1, 'chrY', undef],
# 2:5000-5534 - chr17
[ 'chr17/5534-5000', 5000, 5534, -1, 'chr17', undef],
# 3:19000-19537 - chr7
[ 'chr7/19537-19000', 19000, 19537, -1, 'chr7', undef],
);
for my $pos (1..3) {
my $seq = $aln->get_seq_by_pos($pos);
my @seq_data = @{shift @test_data};
is $seq->get_nse, shift @seq_data, "xmfa input test ";
is $seq->start, shift @seq_data, "xmfa input test for start";
is $seq->end, shift @seq_data, "xmfa input test for end";
is $seq->strand, shift @seq_data, "xmfa strand test";
is $seq->display_id, shift @seq_data, "xmfa input test for id";
is $seq->description, shift @seq_data, "xmfa input test for id";
}
# test aln
is $aln->score, 111, 'xmfa alignment score';
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is $aln->get_seq_by_pos(1)->get_nse, 'chrY/1000-1059',
"xmfa input test ";
is $aln->get_seq_by_pos(1)->strand, 1,
"xmfa strand";
is ($aln->get_seq_by_pos(2)->description, undef,
"xmfa input test for description");
is ($aln->get_seq_by_pos(3)->display_id, 'chr12',
"xmfa input test for id");
is ($aln->get_seq_by_pos(2)->start, 6000,
"xmfa input test for end");
is ($aln->get_seq_by_pos(1)->end, 1059,
"xmfa input test for end");
is ($aln->score, 11, 'xmfa alignment score');
$strout = Bio::AlignIO->new(
'-file' => ">".test_output_file(),
'-format' => 'xmfa');
$status = $strout->write_aln($aln);
is $status, 1,"xmfa output test";
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