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#-*-Perl-*-
## Bioperl Test Harness Script for Modules
# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.t'
use strict;
use lib '.','./blib/lib';
BEGIN {
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan test => 12;
}
use Bio::DB::Fasta;
use Bio::Root::IO;
my $db = Bio::DB::Fasta->new(Bio::Root::IO->catfile(qw(. t data dbfa)),
-reindex=>1);
ok($db);
ok($db->length('CEESC13F') > 0);
ok(length $db->seq('CEESC13F:1,10') == 10);
ok(length $db->seq('AW057119',1,10) == 10);
my $primary_seq = $db->get_Seq_by_id('AW057119');
ok($primary_seq);
ok(length($primary_seq->seq) > 0);
ok(!defined $db->get_Seq_by_id('foobarbaz'));
undef $db;
undef $primary_seq;
my (%h,$dna1,$dna2);
ok(tie(%h,'Bio::DB::Fasta',Bio::Root::IO->catfile(qw(. t data dbfa))));
ok($h{'AW057146'});
ok($dna1 = $h{'AW057146:1,10'});
ok($dna2 = $h{'AW057146:10,1'});
my $revcom = reverse $dna1;
$revcom =~ tr/gatcGATC/ctagCTAG/;
ok($dna2 eq $revcom);
END {
unlink Bio::Root::IO->catfile(qw(t data dbfa directory.index));
unlink Bio::Root::IO->catfile(qw(t data dbfa directory.index.dir));
unlink Bio::Root::IO->catfile(qw(t data dbfa directory.index.pag));
}
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