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|
use strict;
BEGIN {
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 12;
}
use Bio::Root::IO;
use Bio::Index::Fasta;
use Bio::Index::SwissPfam;
use Bio::Index::EMBL;
use Bio::Index::GenBank;
use Bio::Index::Swissprot;
use Bio::DB::InMemoryCache;
eval {foobar();
require Bio::DB::FileCache;
};
use vars qw ($dir);
($Bio::Root::IO::FILESPECLOADED && File::Spec->can('cwd') && ($dir = File::Spec->cwd) ) ||
($dir = `pwd`) || ($dir = '.');
END { unlink qw( Wibbl Wibbl2 Wibbl3 Wibbl4 Wibbl5); }
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" );
{
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 = $stream->next_primary_seq ) {
unless ($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" );
}
{
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" );
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" );
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" );
ok ($gb_ind->fetch('AI129902')->length, 37);
}
my $cache = Bio::DB::InMemoryCache->new( -seqdb => $gb_ind );
ok ( $cache->get_Seq_by_id('AI129902') );
if (Bio::DB::FileCache->can('new')) {
$cache = Bio::DB::FileCache->new($gb_ind);
ok ($cache->get_Seq_by_id('AI129902') );
} else {
skip('Bio::DB::FileCache not loaded because one or more of Storable, DB_File or File::Temp not installed',1);
}
|
