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
93
94
95
96
97
98
99
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqDiff.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 44);
use_ok('Bio::Variation::SeqDiff');
use_ok('Bio::Variation::DNAMutation');
use_ok('Bio::Variation::Allele');
}
my ($obj, $mm, $aa, $dna, $m);
ok $obj = Bio::Variation::SeqDiff->new();
ok $obj->id('id');
is $obj->id, 'id';
ok $obj->sysname('sysname');
is $obj->sysname, 'sysname';
$obj->trivname('trivname');
is $obj->trivname, 'trivname';
ok $obj->chromosome('chr');
is $obj->chromosome, 'chr';
ok $obj->description('desc');
is $obj->description, 'desc';
ok $obj->numbering('numbering');
is $obj->numbering, 'numbering';
ok $obj->offset(100);
is $obj->offset, 100;
# 12345678901234567890
ok $obj->dna_ori ('gctgctgatcgatcgtagctagctag');
is $obj->dna_ori, 'gctgctgatcgatcgtagctagctag';
# generate mutated DNA seq from the mutation
ok $m = Bio::Variation::DNAMutation->new(-isMutation => 1, -start=>14, -end=>14);
ok $a = Bio::Variation::Allele->new(-seq=>'c');
$b = Bio::Variation::Allele->new(-seq=>'g');
ok $m->allele_ori($a);
ok $m->allele_mut($b);
ok $obj->add_Variant($m);
my $m2 = Bio::Variation::DNAMutation->new(-isMutation => 1, -start=>19, -end=>19);
my $a2 = Bio::Variation::Allele->new(-seq=>'c');
my $b2 = Bio::Variation::Allele->new(-seq=>'g');
$m2->allele_ori($a2);
$m2->allele_mut($b2);
$obj->add_Variant($m2);
#ok $obj->dna_mut('gctgctgatcggtcgtagctagctag');
is $obj->dna_mut, 'gctgctgatcgatggtaggtagctag';
ok $obj->rna_ori('gctgctgatcgatcgtagctagctag');
is $obj->rna_ori, 'gctgctgatcgatcgtagctagctag';
$obj->rna_mut('gctgctgatcgatcgtagctagctag');
is $obj->rna_mut, 'gctgctgatcgatcgtagctagctag';
ok $obj->aa_ori('MHYTRD');
is $obj->aa_ori, 'MHYTRD';
ok $obj->aa_mut('MHGTRD');
is $obj->aa_mut, 'MHGTRD';
foreach $mm ( $obj->each_Variant ) {
$mm->primary_tag('a');
isa_ok($mm,'Bio::Variation::VariantI');
}
ok $obj->gene_symbol('fos');
is $obj->gene_symbol, 'fos';
ok $obj->rna_offset(10);
is $obj->rna_offset, 10;
ok $obj->rna_id('transcript#3');
is $obj->rna_id, 'transcript#3';
ok $dna = $obj->seqobj('dna_ori');
isa_ok($dna,'Bio::PrimarySeq');
$obj->aa_mut('');
$aa = $obj->seqobj('aa_mut');
ok not defined $aa;
eval {
$dna = $obj->seqobj('dna_ri');
};
ok $@;
|
