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
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: arp.t 14971 2008-10-28 16:08:52Z cjfields $
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 48,
-requires_module => 'Data::Stag');
use_ok('Bio::AlignIO::arp');
}
my $DEBUG = test_debug();
my ($str,$aln,$strout,$status);
# ARP format
$str = Bio::AlignIO ->new(
'-file' => test_input_file("testaln.arp"),
-verbose => 1,
'-format' => 'arp');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, '01/1-399','ARP get_nse()');
is($aln->get_seq_by_pos(1)->length, '407');
is($aln->num_sequences, 60,'ARP num_sequences()');
is($aln->id, 'Mandenka', 'ARP id()');
is($aln->description, 'mtDNA sequences in the Senegalese Mandenka (hypervariable region 1)', 'ARP description()');
my $coll = $aln->annotation;
isa_ok($coll, 'Bio::AnnotationCollectionI');
my ($ann) = $coll->get_Annotations('Samples');
isa_ok($ann, 'Bio::AnnotationI');
my %nodes = $ann->pairs;
is(keys %nodes, 60);
is($nodes{'03'}, 10);
is(($coll->get_Annotations('DataType'))[0]->value,'DNA');
is(($coll->get_Annotations('MissingData'))[0]->value,'?');
$str = Bio::AlignIO->new(
'-file' => test_input_file("testaln2.arp"),
'-format' => 'arp');
isa_ok($str,'Bio::AlignIO');
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(1)->get_nse, '000/1-29','ARP get_nse()');
is($aln->num_sequences, 3,'ARP num_sequences()');
is($aln->id, 'Population 1', 'ARP id()');
is($aln->description, 'An example of DNA sequence data', 'ARP description()');
$coll = $aln->annotation;
isa_ok($coll, 'Bio::AnnotationCollectionI');
($ann) = $coll->get_Annotations('Samples');
isa_ok($ann, 'Bio::AnnotationI');
%nodes = $ann->pairs;
is(keys %nodes, 3);
is($nodes{'001'}, 1);
is(($coll->get_Annotations('DataType'))[0]->value, 'DNA');
is(($coll->get_Annotations('SampleSize'))[0]->value, 6);
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(2)->get_nse, '001/1-29','ARP get_nse()');
is($aln->num_sequences, 8,'ARP num_sequences()');
is($aln->id, 'Population 2', 'ARP id()');
is($aln->description, 'An example of DNA sequence data', 'ARP description()');
$coll = $aln->annotation;
isa_ok($coll, 'Bio::AnnotationCollectionI');
($ann) = $coll->get_Annotations('Samples');
isa_ok($ann, 'Bio::AnnotationI');
%nodes = $ann->pairs;
is(keys %nodes, 8);
is($nodes{'001'}, 1);
is(($coll->get_Annotations('DataType'))[0]->value, 'DNA');
is(($coll->get_Annotations('SampleSize'))[0]->value, 8);
$aln = $str->next_aln();
isa_ok($aln,'Bio::Align::AlignI');
is($aln->get_seq_by_pos(2)->get_nse, '024/1-29','ARP get_nse()');
is($aln->num_sequences, 6,'ARP num_sequences()');
is($aln->id, 'Population 3', 'ARP id()');
is($aln->description, 'An example of DNA sequence data', 'ARP description()');
$coll = $aln->annotation;
isa_ok($coll, 'Bio::AnnotationCollectionI');
($ann) = $coll->get_Annotations('Samples');
isa_ok($ann, 'Bio::AnnotationI');
%nodes = $ann->pairs;
is(keys %nodes, 6);
is($nodes{'024'}, 1);
is(($coll->get_Annotations('DataType'))[0]->value, 'DNA');
is(($coll->get_Annotations('SampleSize'))[0]->value, 6);
|
