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
|
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: qual.t,v 1.4 2001/10/12 22:24:08 matsallac Exp $
#
use strict;
use vars qw($DEBUG);
$DEBUG = $ENV{'BIOPERLDEBUG'};
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 => 12;
}
END {
unlink qw(write_qual.qual );
}
print("Checking if the Bio::SeqIO::Qual module could be used, even though it shouldn't be directly use'd...\n") if ( $DEBUG );
# test 1
use Bio::SeqIO::qual;
ok(1);
print("Checking to see if PrimaryQual.pm can be used...\n") if ( $DEBUG );
use Bio::Seq::PrimaryQual;
ok(1);
print("Checking to see if PrimaryQual objects can be created from a file...\n") if ( $DEBUG );
my $in_qual = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile("t","data",
"qualfile.qual"),
'-format' => 'qual');
ok(1);
my @quals;
print("I saw these in qualfile.qual:\n") if $DEBUG;
my $first = 1;
while ( my $qual = $in_qual->next_seq() ) {
# ::dumpValue($qual);
ok(1);
@quals = @{$qual->qual()};
if( $DEBUG ) {
print($qual->id()."\n");
print("(".scalar(@quals).") quality values.\n");
}
if( $first ) {
ok(@quals, 484);
}
$first = 0;
}
|
