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
100
101
102
103
104
105
|
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: AAChange.t,v 1.5 2001/08/03 10:11:24 heikki Exp $
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 25;
}
use Bio::Variation::Allele;
use Bio::Variation::AAChange;
use Bio::Variation::RNAChange;
my $obj = Bio::Variation::AAChange -> new;
ok(1);
ok defined $obj;
ok ref($obj), 'Bio::Variation::AAChange';
$obj->start(3);
ok $obj->start, 3;
$obj->end(3);
ok $obj->end, 3;
$obj->length(3);
ok $obj->length, 3;
$obj->strand('1');
ok $obj->strand, '1';
ok $obj->primary_tag, 'Variation';
$obj->source_tag('source');
ok $obj->source_tag, 'source';
$obj->frame(2);
ok $obj->frame,2;
$obj->score(2);
ok $obj->score, 2;
$obj->isMutation(1);
ok $obj->isMutation;
my $a1 = Bio::Variation::Allele->new(-seq => 'V');
$obj->allele_ori($a1);
ok $obj->allele_ori->seq, 'V';
my $a2 = Bio::Variation::Allele->new('-seq' => 'A');
$obj->add_Allele($a2);
ok $obj->allele_mut->seq, 'A';
ok $obj->similarity_score, 0;
$obj->upStreamSeq('upStreamSeq');
ok $obj->upStreamSeq, 'upStreamSeq';
$obj->dnStreamSeq('dnStreamSeq');
ok $obj->dnStreamSeq, 'dnStreamSeq' ;
ok $obj->label, 'substitution, conservative';
$obj->status('proven');
ok $obj->status, 'proven';
$obj->proof('experimental');
ok $obj->proof, 'experimental';
$obj->region('region');
ok $obj->region, 'region';
$obj->region_value('region_value');
ok $obj->region_value, 'region_value';
$obj->numbering('coding');
ok $obj->numbering, 'coding';
my $obj2 = Bio::Variation::RNAChange -> new(-start => 7,
-end => 7,
-cds_end => 100,
-codon_pos => 1,
-upStreamSeq => 'acgcgcgcgc',
-dnStreamSeq => 'acgcgcgcgc'
);
$obj2->label('missense');
$obj->RNAChange($obj2);
ok $obj->trivname, 'V3A', "Trivial name is !". $obj->trivname. "!\n";
$obj->mut_number(2);
ok $obj->mut_number, 2;
|
