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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 lib '.';
use Bio::Root::Test;
test_begin(-tests => 16);
use_ok('Bio::AlignIO::xmfa');
}
my $DEBUG = test_debug();
my ($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');
is $aln->get_seq_by_pos(1)->get_nse, 'chrY/1-598',
"xmfa input test ";
is ($aln->get_seq_by_pos(2)->description, undef,
"xmfa input test for description");
is ($aln->get_seq_by_pos(3)->display_id, 'chr7',
"xmfa input test for id");
is ($aln->get_seq_by_pos(2)->start, 5000,
"xmfa input test for end");
is ($aln->get_seq_by_pos(2)->end, 5534,
"xmfa input test for end");
is ($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(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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