1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: gerp.t,v 1.15 2007/06/27 10:16:38 sendu Exp $
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 33,
-requires_module => 'URI::Escape');
use_ok('Bio::Tools::Phylo::Gerp');
}
ok my $parser = Bio::Tools::Phylo::Gerp->new(-file => test_input_file('ENr111.mfa.example.elems'));
my $count = 0;
my @expected = ([qw(334180 334352 449 1.03744e-165)],
[qw(337735 337915 458.2 5.02405e-164)],
[qw(262604 262861 473.1 3.64789e-117)],
[qw(285427 285608 386.1 8.42494e-113)],
[qw(309563 309744 383.6 2.88895e-111)]);
while (my $feat = $parser->next_result) {
$count++;
my @exp = @{shift(@expected)};
isa_ok $feat, 'Bio::SeqFeature::Generic';
is $feat->source_tag, 'GERP', 'correct source';
is $feat->start, shift(@exp), 'feature start correct';
is $feat->end, shift(@exp), 'feature end correct';
is $feat->score, shift(@exp), 'feature score correct';
my ($p_value) = $feat->annotation->get_Annotations('pvalue');
is ref $p_value ? $p_value->value : $p_value, shift(@exp), 'feature pvalue correct';
}
is $count, 5, "correct number of results parsed out";
|
