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# -*-Perl-*-
# $Id: Index.t,v 1.28 2003/06/10 21:34:57 jason Exp $
use strict;
my $exit;
BEGIN {
eval { require Test; };
use vars qw($NUMTESTS);
$NUMTESTS = 32;
if( $@ ) {
use lib 't';
}
use Test;
$exit = 0;
eval { require Bio::Index::Fasta;
require Bio::Index::SwissPfam;
require Bio::Index::EMBL;
require Bio::Index::GenBank;
require Bio::Index::Swissprot;
require DB_File;
};
if( $@ ) {
$exit = 1;
}
plan tests => $NUMTESTS;
}
END {
foreach ( $Test::ntest..$NUMTESTS) {
skip('DB_File not loaded because one or more of Storable, DB_File or File::Temp not installed',1);
}
foreach my $root ( qw( Wibbl Wibbl2 Wibbl3 Wibbl4 Wibbl5
) ) {
if( -e "$root" ) { unlink $root;}
if( -e "$root.pag") { unlink "$root.pag";}
if( -e "$root.dir") { unlink "$root.dir";}
}
}
exit(0) if $exit;
use Bio::Root::IO;
use Bio::DB::InMemoryCache;
eval { require Bio::DB::FileCache };
use vars qw ($dir);
($Bio::Root::IO::FILESPECLOADED && File::Spec->can('cwd') &&
($dir = File::Spec->cwd) ) ||
($dir = `pwd`) || ($dir = '.');
chomp( $dir );
{
my $ind = Bio::Index::Fasta->new(-filename => 'Wibbl',
-write_flag => 1,
-verbose => 0);
$ind->make_index(Bio::Root::IO->catfile($dir,"t","data","multifa.seq"));
$ind->make_index(Bio::Root::IO->catfile($dir,"t","data","seqs.fas"));
$ind->make_index(Bio::Root::IO->catfile($dir,"t","data","multi_1.fa"));
}
ok ( -e "Wibbl" || -e "Wibbl.pag" );
{
my %t_seq = (
HSEARLOBE => 321,
HSMETOO => 134,
MMWHISK => 62,
'gi|238775|bbs|65126' => 70,
);
my $ind = Bio::Index::Abstract->new(-FILENAME => 'Wibbl');
my $ok_3 = 1;
while (my($name, $length) = each %t_seq) {
my $seq = $ind->fetch($name);
if( defined($seq) and $seq->isa('Bio::SeqI') ) {
my $r_length = $seq->length;
unless ($r_length == $length) {
warn "$name - retrieved length '$r_length' doesn't match known length '$length'\n";
$ok_3 = 0;
}
} else {
warn "Didn't get sequence '$name' from index\n";
$ok_3 = 0;
}
}
ok $ok_3;
my $stream = $ind->get_PrimarySeq_stream();
my $ok_4 = 1;
while( my $seq2 = $stream->next_seq ) {
unless ($seq2->isa('Bio::PrimarySeqI')) {
$ok_4 = 0;
last; # no point continuing...
}
}
ok $ok_4;
}
{
my $ind = Bio::Index::SwissPfam->new(-filename=>'Wibbl2',
-write_flag=>1);
$ind->make_index(Bio::Root::IO->catfile($dir,"t","data","swisspfam.data"));
ok ( -e "Wibbl2" || -e "Wibbl2.pag" );
}
{
my $ind = Bio::Index::EMBL->new(-filename=>'Wibbl3',
-write_flag=>1);
$ind->make_index(Bio::Root::IO->catfile($dir,"t","data","test.embl"));
ok ( -e "Wibbl3" || -e "Wibbl3.pag" );
ok $ind->fetch('AL031232')->length, 4870;
}
{
my $ind = Bio::Index::Swissprot->new(-filename=>'Wibbl4',
-write_flag=>1);
$ind->make_index(Bio::Root::IO->catfile($dir,"t","data","roa1.swiss"));
ok ( -e "Wibbl4" || -e "Wibbl4.pag" );
ok ($ind->fetch('P09651')->display_id(), 'ROA1_HUMAN');
}
my $gb_ind;
{
$gb_ind = Bio::Index::GenBank->new(-filename=>'Wibbl5',
-write_flag=>1,
-verbose => 0);
$gb_ind->make_index(Bio::Root::IO->catfile($dir,"t","data","roa1.genbank"));
ok ( -e "Wibbl5" || -e "Wibbl5.pag" );
my $seq =$gb_ind->fetch('AI129902');
ok ($seq->length, 37);
ok ($seq->species->binomial, 'Homo sapiens');
}
my $cache = Bio::DB::InMemoryCache->new( -seqdb => $gb_ind );
ok ( $cache->get_Seq_by_id('AI129902') );
if (Bio::DB::FileCache->can('new')) {
$cache = Bio::DB::FileCache->new(-seqdb => $gb_ind,
-keep => 1,
-file => 'filecache.idx');
my $seq = $cache->get_Seq_by_id('AI129902');
ok ( $seq);
ok ( $seq->length, 37);
ok ( lc($seq->seq()), 'ctccgcgccaactccccccaccccccccccacacccc');
my ( $f1 ) = $seq->get_SeqFeatures();
ok ( ($f1->each_tag_value('sex'))[0], 'female');
ok ( ($f1->each_tag_value('lab_host'))[0], 'DH10B');
my $species = $seq->species;
ok( $species );
ok( $species->binomial, 'Homo sapiens');
ok( $species->species(), 'sapiens');
ok( $species->genus(), 'Homo');
ok ($species->common_name(), 'human');
$cache = undef;
$cache = Bio::DB::FileCache->new(-seqdb => $gb_ind,
-keep => 0,
-file => 'filecache.idx');
$seq = $cache->get_Seq_by_id('AI129902');
ok ( $seq);
ok ( $seq->length, 37);
ok ( lc($seq->seq()), 'ctccgcgccaactccccccaccccccccccacacccc');
( $f1 ) = $seq->get_SeqFeatures();
ok ( ($f1->each_tag_value('sex'))[0], 'female');
ok ( ($f1->each_tag_value('lab_host'))[0], 'DH10B');
$species = $seq->species;
ok( $species );
ok( $species->binomial, 'Homo sapiens');
ok( $species->species(), 'sapiens');
ok( $species->genus(), 'Homo');
ok ($species->common_name(), 'human');
} else {
skip('Bio::DB::FileCache not loaded because one or more of Storable, DB_File or File::Temp not installed',1);
}
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