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
|
##-*-Perl-*-
# $Id: Registry.t,v 1.5 2003/11/17 15:37:19 bosborne Exp $
# test for Bio::DB::Registry, Flat::BinarySearch, and Flat::BDB
# written by Brian Osborne
use strict;
my $old_search_path;
use vars qw($old_search_path $have_DB_File);
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't','..';
}
use Test;
$have_DB_File = 0;
$old_search_path = $ENV{OBDA_SEARCH_PATH} if defined $ENV{OBDA_SEARCH_PATH};
eval {require DB_File;
require BerkeleyDB;};
if ($@) {
$ENV{OBDA_SEARCH_PATH} = 't/data/registry/flat';
print STDERR "DB_File and BerkeleyDB not found. Skipping DB_File tests\n";
plan tests => 6;
} else {
$have_DB_File = 1;
$ENV{OBDA_SEARCH_PATH} = 't/data/registry/flat;t/data/registry/bdb';
plan tests => 11;
}
}
use Bio::DB::Registry;
use Bio::DB::Flat;
use Bio::Root::IO;
my $tmpdir = "t/tmp";
mkdir($tmpdir,0777);
my $flat = Bio::DB::Flat->new(-directory => $tmpdir,
-dbname => 'testflat',
-format => 'fasta',
-index => 'binarysearch',
-write_flag => 1 );
my $entries = $flat->build_index("t/data/cysprot.fa");
ok $entries == 7;
if ($have_DB_File) {
my $bdb = Bio::DB::Flat->new(-directory => $tmpdir,
-dbname => 'testbdb',
-format => 'fasta',
-index => 'bdb',
-write_flag => 1 );
$entries = $bdb->build_index("t/data/cysprot.fa");
ok $entries == 7;
}
my $registry = Bio::DB::Registry->new;
ok defined($registry);
my @available_services = $registry->services;
if ($have_DB_File) {
ok grep /testbdb/,@available_services;
}
ok grep /testflat/,@available_services;
my $db = $registry->get_database('testflat');
ok defined($db);
my $seq = $db->get_Seq_by_id("ALEU_HORVU");
ok defined($seq);
my $sequence = $seq->seq;
ok $sequence eq "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
if ($have_DB_File) {
$db = $registry->get_database('testbdb');
ok defined($db);
$seq = $db->get_Seq_by_id("ALEU_HORVU");
ok defined($seq);
$sequence = $seq->seq;
ok $sequence eq "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
}
END { cleanup(); }
sub cleanup {
eval {
Bio::Root::IO->rmtree($tmpdir) if (-d $tmpdir);
};
}
__END__
|
