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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: BlastIndex.t,v 1.6 2003/05/19 16:27:06 jason Exp $
# 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 vars qw($NUMTESTS);
my $error;
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; };
$error = 0;
if( $@ ) {
use lib 't';
}
use Test;
$NUMTESTS = 13;
plan tests => $NUMTESTS;
eval { require 'IO/String.pm' };
if( $@ ) {
for( $Test::ntest..$NUMTESTS ) {
skip("IO::String not installed. This means the Bio::Index::Blast modules are not usable. Skipping tests",1);
}
$error = 1;
}
}
if( $error == 1 ) {
exit(0);
}
require Bio::SearchIO;
require Bio::Index::Blast;
require Bio::Root::IO;
use Cwd;
END { unlink qw( Wibbl Wibbl.pag Wibbl.dir ); }
ok(1);
my $index = new Bio::Index::Blast(-filename => 'Wibbl',
-write_flag => 1);
ok($index);
$index->make_index(Bio::Root::IO->catfile(cwd,"t","data","multi_blast.bls"));
($index->dbm_package eq 'SDBM_File') ?
(ok(-e "Wibbl.pag" && -e "Wibbl.dir")) :
(ok(-e "Wibbl"));
foreach my $id ( qw(CATH_RAT PAPA_CARPA) ) {
my $fh = $index->get_stream($id);
ok($fh);
ok( ! eof($fh) );
my $report = new Bio::SearchIO(-noclose => 1,
-format => 'blast',
-fh => $fh);
my $result = $report->next_result;
ok($result->query_name, qr/$id/);
ok( $result->next_hit);
ok( $index->fetch_report($id)->query_name, qr/$id/);
}
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