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# -*-Perl-*- Test Harness script for Bioperl
# $Id: Blast.t 16293 2009-10-27 20:03:02Z cjfields $
use strict;
use File::Spec;
use File::Temp;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 27,
-requires_module => 'IO::String');
use_ok('Cwd');
use_ok('Bio::SearchIO');
use_ok('Bio::Index::BlastTable');
}
# -m 9 -m 8
my @test_cases = qw(multi.blast.m9 multi.blast.m8);
for my $file (@test_cases) {
my $dir = File::Temp->newdir();
my $basename = 'Wibbl';
my $filepath = File::Spec->catfile($dir, $basename);
my $index = Bio::Index::BlastTable->new(-filename => $filepath,
-write_flag => 1);
ok($index);
$index->id_parser(\&my_id_parser);
$index->make_index(test_input_file($file));
($index->dbm_package eq 'SDBM_File') ?
(ok(-e "$filepath.pag" && -e "$filepath.dir")) :
(ok(-e $filepath));
foreach my $id ( qw(SP130_MOUSE IKZF1_MOUSE) ) {
my $fh = $index->get_stream($id);
ok($fh);
ok( ! eof($fh) );
my $report = Bio::SearchIO->new(-noclose => 1,
-format => 'blasttable',
-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/$id/);
}
}
# test id_parser
sub my_id_parser {
if ($_[0] =~ /^\S+\|(\S+)/) {
return $1;
} else {
return;
}
}
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