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
|
# -*-Perl-*- Test Harness script for Bioperl
# $Id: Flat.t 15178 2008-12-16 12:48:21Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 24,
-requires_module => 'DB_File');
use_ok('Bio::DB::Flat');
}
my $verbose = test_debug();
# First of all we need to create an flat db
my $tmpdir = test_output_dir();
my $db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'bdb',
-dbname => 'mydb',
-format => 'fasta',
-verbose => $verbose,
-write_flag => 1 );
ok($db);
my $dir = test_input_file('AAC12660.fa');
my $result = $db->build_index(glob($dir));
ok($result);
# Now let's get the sequence out again
my $seq = $db->get_Seq_by_id('AAC12660');
ok($seq);
is($seq->length,504);
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'bdb',
-format => 'embl',
-dbname => 'myembl',
-verbose => $verbose,
-write_flag => 1 );
$dir= test_input_file('factor7.embl');
$result = $db->build_index(glob($dir));
ok($result);
$seq = $db->get_Seq_by_id('HSCFVII');
ok($seq);
is($seq->length,12850);
# deal with wantarray conditions
$seq = $db->get_Seq_by_acc('J02933');
ok($seq && ref($seq));
is($seq->length,12850);
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'binarysearch',
-format => 'fasta',
-dbname => 'mybinfa',
-verbose => $verbose,
-write_flag => 1
);
$dir= test_input_file('dbfa', '1.fa');
$result = $db->build_index($dir);
ok($result);
$seq = $db->get_Seq_by_id('AW057119');
ok($seq);
is($seq->length,808);
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'binarysearch',
-format => 'swiss',
-dbname => 'mybinswiss',
-verbose => $verbose,
-write_flag => 1
);
$dir= test_input_file('swiss.dat');
$result = $db->build_index($dir);
ok($result);
$seq = $db->get_Seq_by_id('ACON_CAEEL');
ok($seq);
is($seq->length,788);
$seq = $db->get_Seq_by_id('ACON_CAEEL');
ok($seq && ref($seq));
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'binarysearch',
-format => 'fasta',
-dbname => 'myfasta',
-verbose => $verbose,
-write_flag => 1 );
$dir = test_input_file('tmp.fst');
$result = $db->build_index(glob($dir));
ok($result);
$seq = $db->get_Seq_by_id('TEST00004');
is($seq->length,98);
undef $db;
$db = Bio::DB::Flat->new(-directory => $tmpdir,
-index => 'bdb',
-format => 'fasta',
-dbname => 'mybfasta',
-verbose => $verbose,
-write_flag => 1 );
$dir = test_input_file('tmp.fst');
$result = $db->build_index(glob($dir));
ok($result);
for my $id ( qw(TEST00001 TEST00002 TEST00003 TEST00004) ) {
$seq = $db->get_Seq_by_id($id);
is($seq->length,98);
}
|
