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
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: SeqAnalysisParser.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::Factory::SeqAnalysisParserFactory');
use_ok('Bio::SeqIO');
}
my ($seqio,$seq,$factory,$parser, $gene_seen, $exon_seen);
$seqio = Bio::SeqIO->new('-format'=>'fasta', '-file' => test_input_file('genomic-seq.fasta'));
isa_ok $seqio, 'Bio::SeqIO';
$seq = $seqio->next_seq;
isa_ok $seq, 'Bio::PrimarySeqI';
$factory = Bio::Factory::SeqAnalysisParserFactory->new();
# let's test the genscan factory
$parser = $factory->get_parser(-input => test_input_file('genomic-seq.genscan'),
-method => 'genscan');
isa_ok $parser, 'Bio::SeqAnalysisParserI';
while( my $feat = $parser->next_feature() ){
$seq->add_SeqFeature($feat);
}
($gene_seen, $exon_seen) = (0,0);
foreach my $feat ( $seq->top_SeqFeatures() ) {
if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
foreach my $exon ( $feat->exons ) {
$exon_seen++;
}
$gene_seen++;
}
}
is $exon_seen, 37;
is $gene_seen, 3;
# let's test the mzef factory
$parser = $factory->get_parser(-input => test_input_file('genomic-seq.mzef'),
-method=> 'mzef');
$seqio = Bio::SeqIO->new('-format'=>'fasta', '-file' => test_input_file('genomic-seq.fasta'));
ok $seq = $seqio->next_seq();
isa_ok $seq, 'Bio::PrimarySeqI';
isa_ok $parser, 'Bio::SeqAnalysisParserI';
while( my $feat = $parser->next_feature() ){
$seq->add_SeqFeature($feat);
}
($gene_seen, $exon_seen) = (0,0);
foreach my $feat ( $seq->top_SeqFeatures() ) {
if( $feat->isa("Bio::Tools::Prediction::Gene") ) {
foreach my $exon ( $feat->exons ) {
$exon_seen++;
}
$gene_seen++;
}
}
is $exon_seen, 23;
is $gene_seen, 1;
# let's test the ePCR factory
$parser = $factory->get_parser(-input => test_input_file('genomic-seq.epcr'),
-method => 'epcr');
$seq->flush_SeqFeatures;
isa_ok $parser, 'Bio::SeqAnalysisParserI';
while( my $feat = $parser->next_feature() ){
$seq->add_SeqFeature($feat);
}
is $seq->top_SeqFeatures(), 7;
|
