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
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: tRNAscanSE.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 14);
use_ok('Bio::Tools::tRNAscanSE');
}
my $verbose = test_debug();
my $parser = Bio::Tools::tRNAscanSE->new(-verbose => $verbose,
-file => test_input_file('yeast.tRNAscanSE'));
isa_ok($parser, 'Bio::Tools::tRNAscanSE') ;
my @genes;
while( my $gene = $parser->next_prediction ) {
push @genes, $gene;
}
is (scalar(@genes), 287);
is($genes[2]->seq_id, 'I', 'seq_id');
my ($codon) = $genes[2]->get_tag_values('Codon');
is($codon, 'TTG', 'codon');
is($genes[2]->start, 181135, 'start');
is($genes[2]->end, 181248, 'end');
is($genes[2]->strand, 1, 'strand');
my @exons = $genes[2]->get_SeqFeatures ;
is ( scalar(@exons), 2, 'exons' );
is($exons[0]->end,181172, 'end' );
is($exons[0]->start,$genes[2]->start, 'start');
is($exons[1]->start,181205, 'start');
is($exons[1]->end,$genes[2]->end, 'end');
is($exons[0]->seq_id, $genes[2]->seq_id, 'seq_id');
|
