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
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 70);
use_ok('Bio::SeqIO');
use_ok('Bio::Seq::Quality');
use_ok('Bio::Seq::PrimaryQual');
}
my $DEBUG = test_debug();
my $verbose = -1 unless $DEBUG;
# redirect STDERR to STDOUT
open (STDERR, ">&STDOUT");
my $string_quals = "10 20 30 40 50 40 30 20 10";
print("Quals are $string_quals\n") if($DEBUG);
ok my $qualobj = Bio::Seq::PrimaryQual->new(
-qual => $string_quals,
-id => 'QualityFragment-12',
-accession_number => 'X78121',
);
is $qualobj->display_id, 'QualityFragment-12';
is $qualobj->accession_number, 'X78121';
my @q2 = split / /, $string_quals;
$qualobj = Bio::Seq::PrimaryQual->new(
-qual => \@q2,
-primary_id => 'chads primary_id',
-desc => 'chads desc',
-accession_number => 'chads accession_number',
-id => 'chads id',
-header => 'chads header'
);
is $qualobj->primary_id, 'chads primary_id';
isa_ok $qualobj->qual(), 'ARRAY';
my $newqualstring = "50 90 1000 20 12 0 0";
ok $qualobj->qual($newqualstring);
is join(' ', @{$qualobj->qual()}), $newqualstring;
my @newqualarray = split / /,$newqualstring;
ok $qualobj->qual(\@newqualarray);
is join(' ', @{$qualobj->qual()}), $newqualstring;
is $qualobj->validate_qual($string_quals ), 1;
is $qualobj->validate_qual("" ), 1;
is $qualobj->validate_qual("0" ), 1;
is $qualobj->validate_qual(undef ), 1;
is $qualobj->validate_qual(" " ), 1;
is $qualobj->validate_qual("10 20 30 30" ), 1;
is $qualobj->validate_qual(" 20 9 5 " ), 1;
is $qualobj->validate_qual("+1 9.3 50e-1"), 1;
is $qualobj->validate_qual(" 4" ), 1;
is $qualobj->validate_qual("chad" ), 0;
is $qualobj->validate_qual("10 one" ), 0;
ok $qualobj->qual("10 20 30 30");
ok $qualobj->qual("+1 9.3 50e-1");
throws_ok { $qualobj->qual("chad"); } qr/.+/;
throws_ok { $qualobj->validate_qual("chad", 1) } qr/.+/;
ok $qualobj->qual("4 10");
is $qualobj->length(), 2;
$qualobj->qual("10 20 30 40 50 40 30 20 10");
ok my @subquals = @{$qualobj->subqual(3,6);};
is @subquals, 4;
is "30 20 10", join(' ',@{$qualobj->subqual(7,9)});
throws_ok { $qualobj->subqual(-1,6); } qr/EX/;
ok $qualobj->subqual(1,6);
ok $qualobj->subqual(1,9);
throws_ok { $qualobj->subqual(9,1); } qr/EX/;
is $qualobj->display_id(), "chads id";
is $qualobj->display_id("chads new display_id"), "chads new display_id";
is $qualobj->display_id(), "chads new display_id";
is $qualobj->accession_number(), "chads accession_number";
is $qualobj->accession_number("chads new accession_number"), "chads new accession_number";
is $qualobj->accession_number(), "chads new accession_number";
is $qualobj->primary_id(), "chads primary_id";
is $qualobj->primary_id("chads new primary_id"), "chads new primary_id";
is $qualobj->primary_id(), "chads new primary_id";
is $qualobj->desc(), "chads desc";
is $qualobj->desc("chads new desc"), "chads new desc";
is $qualobj->desc(), "chads new desc";
is $qualobj->display_id(), "chads new display_id";
is $qualobj->display_id("chads new id"), ("chads new id");
is $qualobj->display_id(), "chads new id";
is $qualobj->header(), "chads header";
ok my $in_qual = Bio::SeqIO->new(
-file => test_input_file('qualfile.qual'),
-format => 'qual',
-verbose => $verbose,
);
ok my $pq = $in_qual->next_seq();
is $pq->qual()->[99] , '39'; # spot check boundary
is $pq->qual()->[100], '39'; # spot check boundary
ok my $out_qual = Bio::SeqIO->new(
-file => ">".test_output_file(),
-format => 'qual',
-verbose => $verbose,
);
ok $out_qual->write_seq(-source => $pq);
ok my $swq545 = Bio::Seq::Quality->new (
-seq => "ATA",
-qual => $pq
);
ok $out_qual->write_seq(-source => $swq545);
ok $in_qual = Bio::SeqIO->new(
-file => test_input_file('qualfile.qual'),
-format => 'qual',
-verbose => $verbose,
);
ok my $out_qual2 = Bio::SeqIO->new(
-file => ">".test_output_file(),
-format => 'qual',
-verbose => $verbose,
);
while ( my $batch_qual = $in_qual->next_seq() ) {
ok $out_qual2->write_seq(-source => $batch_qual);
}
|
