File: SeqPattern.t

package info (click to toggle)
bioperl 1.0-1
  • links: PTS
  • area: main
  • in suites: woody
  • size: 10,784 kB
  • ctags: 4,962
  • sloc: perl: 70,732; xml: 3,279; lisp: 107; makefile: 53
file content (43 lines) | stat: -rw-r--r-- 1,328 bytes parent folder | download | duplicates (3)
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
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
##

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 => 6;
}

use Bio::Tools::SeqPattern;

my ( $pattern,$pattern_obj,$pattern_obj2, $pattern_obj3);

$pattern     = '(CCCCT)N{1,200}(agyyg)N{1,80}(ag)';
$pattern_obj = new Bio::Tools::SeqPattern(-SEQ =>$pattern, -TYPE =>'dna');
ok defined($pattern_obj) && ref($pattern_obj) && $pattern_obj->isa('Bio::Tools::SeqPattern');

$pattern_obj2  = $pattern_obj->revcom();
ok $pattern_obj2->str, '(CT)N(CRRCT){1,80}N(AGGGG){1,200}';

$pattern_obj3 = $pattern_obj->revcom(1);
ok $pattern_obj3->str, '(CT).{1,80}(C[GA][GA]CT).(AGGGG){1,200}';

$pattern     = '(CCCCT)N{1,200}(agyyg)N{1,80}(bb)'; # test protein object expand
$pattern_obj = new Bio::Tools::SeqPattern(-SEQ =>$pattern, -TYPE =>'protein');
ok defined($pattern_obj) && ref($pattern_obj) && $pattern_obj->isa('Bio::Tools::SeqPattern');

ok $pattern_obj2->expand, '(CT).(C[AG][AG]CT){1,80}.(AGGGG){1,200}';

# amino patterns

$pattern = 'ABZH';
$pattern_obj2 = new Bio::Tools::SeqPattern(-SEQ =>$pattern, 
					   -TYPE =>'amino');
ok $pattern_obj2->expand, 'A[EQ][DN]H';