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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: Exonerate.t,v 1.5 2003/03/29 20:25:02 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'
my $error;
use strict;
use 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( $@ ) {
use lib 't';
}
use vars qw($NTESTS);
$NTESTS = 45;
$error = 0;
use Test;
plan tests => $NTESTS;
}
if( $error == 1 ) {
exit(0);
}
use Bio::SearchIO;
use Bio::Root::IO;
use Bio::SearchIO::Writer::HitTableWriter;
use Bio::SearchIO::Writer::HTMLResultWriter;
ok(1);
my ($searchio, $result,$hit,$hsp);
$searchio = new Bio::SearchIO(-file =>
Bio::Root::IO->catfile(qw(t data
testdat.exonerate)),
-format => 'exonerate');
my @data = ( [qw(ln27 416 Contig124 939
293 416 -1
1 124 1
107 292 -1
178 363 1
66 106 -1
899 939 1
)],
[qw(ln74 644 Contig275 1296
601 644 -1
901 944 1
436 600 -1
998 1162 1
386 435 -1
1247 1296 1
)] );
while( my $r = $searchio->next_result ) {
my $d = shift @data;
ok($r->query_name, shift @$d);
skip( 'no query length available in default output',
$r->query_length, shift @$d);
my $h = $r->next_hit;
ok($h->name, shift @$d);
skip( 'no hit length available in default output',$h->length, shift @$d);
while( my $hsp = $h->next_hsp ) {
ok($hsp->query->start, shift @$d);
ok($hsp->query->end, shift @$d);
ok($hsp->query->strand, shift @$d);
ok($hsp->hit->start, shift @$d);
ok($hsp->hit->end, shift @$d);
ok($hsp->hit->strand, shift @$d);
}
}
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