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# -*-Perl-*- Test Harness script for Bioperl
# $Id: BlastIndex.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 26,
-requires_module => 'IO::String');
use_ok('Cwd');
use_ok('Bio::SearchIO');
use_ok('Bio::Index::Blast');
}
END { unlink qw( Wibbl Wibbl.pag Wibbl.dir Wibbl.index); }
# BLASTP
my $index = Bio::Index::Blast->new(-filename => 'Wibbl',
-write_flag => 1);
ok($index);
$index->make_index(test_input_file('multi_blast.bls'));
($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 = Bio::SearchIO->new(-noclose => 1,
-format => 'blast',
-fh => $fh);
my $result = $report->next_result;
like($result->query_name, qr/$id/);
ok( $result->next_hit);
like( $index->fetch_report($id)->query_name, qr/$id/);
}
# RPS-BLAST
$index = Bio::Index::Blast->new(-filename => 'Wibbl.index',
-write_flag => 1);
ok($index);
$index->make_index(test_input_file('rpsblast.bls'));
foreach my $id ( qw(orf20 orf40) ) {
my $fh = $index->get_stream($id);
ok($fh);
ok( ! eof($fh) );
my $report = Bio::SearchIO->new(-noclose => 1,
-format => 'blast',
-fh => $fh);
my $result = $report->next_result;
like($result->query_name, qr/$id/);
ok( $result->next_hit);
like( $index->fetch_report($id)->query_name, qr/$id/);
}
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