1 # -*-Perl-*- Test Harness script for Bioperl
11 test_begin(-tests => 19);
13 use_ok('Bio::PrimarySeq');
14 use_ok('Bio::Tools::SeqWords');
17 my ($seqobj, $count, $seqobj_stats, $wt);
19 $seqobj = Bio::PrimarySeq->new(-seq=>'ACTGTGGCGTCAACTGACTGGC',
20 -alphabet=>'dna', -id=>'test');
21 ok $seqobj_stats = Bio::Tools::SeqWords->new(-seq=>$seqobj);
22 isa_ok $seqobj_stats, 'Bio::Tools::SeqWords';
24 $count = $seqobj_stats->count_words(4);
25 is $count->{'ACTG'}, 3;
26 is $count->{'TGGC'}, 1;
27 is $count->{'GTCA'}, 1;
29 $count = $seqobj_stats->count_overlap_words(4);
30 is $count->{'ACTG'}, 3;
31 is $count->{'TGGC'}, 2;
32 is $count->{'GTCA'}, 1;
33 is $count->{'GTGG'}, 1;
36 $seqobj = Bio::PrimarySeq->new(-seq=>'MQSERGITIDISLWKFETSKYYVTIDISSLWKF',
37 -alphabet=>'protein', -id=>'test');
38 ok $seqobj_stats = Bio::Tools::SeqWords->new('-seq' => $seqobj);
39 isa_ok $seqobj_stats, 'Bio::Tools::SeqWords';
41 $count = $seqobj_stats->count_words(4);
42 is $count->{'MQSE'}, 1;
43 is $count->{'LWKF'}, 1;
44 is $count->{'IDIS'}, 2;
46 $count = $seqobj_stats->count_overlap_words(4);
47 is $count->{'MQSE'}, 1;
48 is $count->{'LWKF'}, 2;
49 is $count->{'IDIS'}, 2;