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
|
# -*-Perl-*-
use strict;
use vars qw($DEBUG $TESTCOUNT);
my $error;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
$TESTCOUNT = 9;
plan tests => $TESTCOUNT;
$error = 0;
};
if( $error == 1 ) {
exit(0);
}
use Bio::Seq;
use Bio::SeqIO;
my $str = Bio::SeqIO->new( '-file'=> Bio::Root::IO->catfile("t","data",
"U58726.gb"),
'-format' => 'GenBank');
ok $str;
my $seq;
ok ( $seq = $str->next_seq() );
# Here is a cute way to verify the sequence by seeing if the
# the translation matches what is annotated in the file -js
foreach my $ft ( grep { $_->primary_tag eq 'CDS'}
$seq->top_SeqFeatures ) {
if( $ft->has_tag('translation') ) {
my ($translation) = $ft->each_tag_value('translation');
my $t = $ft->spliced_seq();
my $pepseq = $t->translate()->seq();
chop($pepseq);# chop is to remove stop codon
ok($translation,$pepseq);
}
}
eval { require Bio::DB::GenBank };
if( $@ ) {
print STDERR "Skipping remote location tests\n";
for( $Test::ntest..$TESTCOUNT ) {
skip("Not possible to test remote locations without DB access",1);
}
exit(0);
} else {
#my $db = Bio::DB::GenBank->new();
#
#foreach my $ft ( $seq->top_SeqFeatures ) {
# my $t = $ft->spliced_seq();
# print "Got ",$t->seq,"\n";
#}
}
|
