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
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
|
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: DNAMutation.t,v 1.7 2002/03/20 13:08:04 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( $@ ) {
use lib 't';
}
use Test;
plan tests => 36 }
use Bio::Variation::DNAMutation;
use Bio::Variation::Allele;
ok(1);
## End of black magic.
##
## Insert additional test code below but remember to change
## the print "1..x\n" in the BEGIN block to reflect the
## total number of tests that will be run.
my($obj,$a1,$a2,$obj2);
$obj = Bio::Variation::DNAMutation -> new;
ok defined $obj;
$obj->start(3);
ok $obj->start, 3;
$obj->end(3);
ok $obj->end, 3;
$obj->length(2);
ok $obj->length, 2;
$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;
if( $obj->can('dna_mut') ) {
#test gff string
$obj->dna_mut('dna_mut');
ok( $obj->dna_mut,'dna_mut');
}
$a1 = Bio::Variation::Allele->new(-seq => 'c');
$obj->allele_ori($a1);
ok $obj->allele_ori->seq, 'c';
$a2 = Bio::Variation::Allele->new('-seq' => 'g');
$obj->allele_mut($a2);
ok $obj->allele_mut->seq, 'g';
$obj->upStreamSeq('agcacctcccggcgccagtttgctg');
ok $obj->upStreamSeq, 'agcacctcccggcgccagtttgctg';
$obj->dnStreamSeq('tgctgcagcagcagcagcagcagca');
ok $obj->dnStreamSeq, 'tgctgcagcagcagcagcagcagca';
ok $obj->label, 'point, transversion' ;
$obj->status('proven');
ok $obj->status, 'proven';
$obj->proof('experimental');
ok $obj->proof, 'experimental';
ok $obj->restriction_changes, '-BbvI, +BstXI, -Fnu4HI, -TseI';
$obj->region('region');
ok $obj->region, 'region';
$obj->region_value('region_value');
ok $obj->region_value, 'region_value';
$obj->region_dist(-5);
ok $obj->region_dist, -5;
$obj->numbering('coding');
ok $obj->numbering, 'coding';
ok not $obj->CpG;
$obj->mut_number(2);
ok $obj->mut_number, 2;
ok defined ($obj2 = Bio::Variation::DNAMutation -> new
('-mut_number' => 2));
ok $obj2->mut_number, 2;
$obj->isMutation(1);
ok $obj->isMutation;
$obj->add_Allele($a1);
$obj->add_Allele($a2);
ok scalar ($obj->each_Allele), 2;
$obj = Bio::Variation::DNAMutation->new
('-start' => 23,
'-end' => 24,
'-length' => 2,
'-upStreamSeq' => 'gt',
'-dnStreamSeq' => 'at',
'-proof' => 'experimental',
'-isMutation' => 1,
'-mut_number' => 2
);
ok $obj->start(), 23;
ok $obj->end(), 24;
ok $obj->length(), 2;
ok $obj->upStreamSeq(), 'gt';
ok $obj->dnStreamSeq(), 'at';
ok $obj->proof(), 'experimental';
ok $obj->mut_number(), 2;
ok $obj->isMutation;
|
