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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 18);
use_ok('Bio::SeqIO');
use_ok('Bio::Seq::PrimaryQual');
}
my $DEBUG = test_debug();
my $in_qual = Bio::SeqIO->new('-file' => test_input_file('qualfile.qual'),
'-format' => 'qual');
ok($in_qual);
my @quals;
my $first = 1;
while ( my $qual = $in_qual->next_seq() ) {
# ::dumpValue($qual);
isa_ok($qual, 'Bio::Seq::PrimaryQual');
@quals = @{$qual->qual()};
if( $DEBUG ) {
warn($qual->id()."\n");
warn("(".scalar(@quals).") quality values.\n");
}
if( $first ) {
is(@quals, 484);
}
$first = 0;
}
# in October 2004, Carlos Mauricio La Rota posted a problem with descriptions
# this routine is to test that
@quals = 10..20;
# this one has a forced header
my $seq = Bio::Seq::PrimaryQual->new(
-qual => \@quals,
-header => "Hank is a good cat. I gave him a bath yesterday.");
my $out = Bio::SeqIO->new(-file => ">".test_output_file(),
-format => 'qual');
# yes, that works
is $seq->header, 'Hank is a good cat. I gave him a bath yesterday.';
@quals = @{$seq->qual()};
is scalar(@quals), 11;
ok $out->write_seq($seq);
$seq->header('');
is $seq->header, '';
$seq->id('Hank1');
is $seq->id, 'Hank1';
# yes, that works
ok $out->write_seq($seq);
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