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
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: SiRNA.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 11);
use_ok('Bio::Tools::SiRNA');
use_ok('Bio::Seq');
use_ok('Bio::SeqIO');
}
my $DEBUG = test_debug();
my $input = Bio::SeqIO->new( -file => test_input_file('NM_002254.gb'),
-format => 'Genbank' );
my $seq = $input->next_seq;
isa_ok( $input, 'Bio::SeqIO' ) ;
#object creation
my $sirna = Bio::Tools::SiRNA->new( -target => $seq,
);
isa_ok( $sirna, 'Bio::Tools::SiRNA' ) ;
# first test - cds only
my @pairs = $sirna->design;
is ( scalar(@pairs), 65, "CDS only: got ". scalar(@pairs) );
# next test - include 3prime utr
my @feats = $seq->remove_SeqFeatures;
foreach my $feat (@feats) {
$seq->add_SeqFeature($feat) unless
($feat->primary_tag eq 'Target' or $feat->isa('Bio::SeqFeature::SiRNA::Pair'));
}
ok( $sirna->include_3pr(1) ) ;
@pairs = $sirna->design;
print "With 3p UTR: got ",scalar(@pairs),"\n" if $DEBUG;
is( scalar(@pairs), 140 );
#third test - naked sequence
my $newseq = Bio::Seq->new( -seq => $seq->seq);
isa_ok($newseq, 'Bio::Seq') ;
ok( $sirna->target($newseq) );
@pairs = $sirna->design;
print "Bare sequence: got ",scalar(@pairs),"\n" if $DEBUG;
is ( scalar(@pairs), 142 ) ;
|
