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# -*-Perl-*- Test Harness script for Bioperl
# $Id$
use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 28);
use_ok('Bio::Tools::RepeatMasker');
}
my $inputfilename = test_input_file('repeatmasker.fa.out');
my $parser = Bio::Tools::RepeatMasker->new(-file => $inputfilename);
{
my $rpt = $parser->next_result;
is ($rpt->feature1->seq_id, "contig11600");
is ($rpt->feature1->start, 1337);
is ($rpt->feature1->end, 1407);
is ($rpt->feature1->strand, 1);
is ($rpt->feature1->primary_tag, "Simple_repeat");
is ($rpt->feature1->source_tag, "RepeatMasker");
is (scalar $rpt->feature1->get_tag_values('Target'), 3);
is ($rpt->feature2->seq_id, "(TTAGGG)n");
is ($rpt->feature2->start, 2);
is ($rpt->feature2->end, 76);
is ($rpt->feature1->primary_tag, "Simple_repeat");
is ($rpt->feature1->source_tag, "RepeatMasker");
is (scalar $rpt->feature2->get_tag_values('Target'), 3);
}
$parser->next_result for 1,2,3;
{
my $rpt = $parser->next_result;
is ($rpt->feature1->seq_id, "SL2.30ch10");
is ($rpt->feature1->start, 38849);
is ($rpt->feature1->end, 38940);
is ($rpt->feature1->strand, -1);
is ($rpt->feature1->primary_tag, "LTR");
is ($rpt->feature1->source_tag, "RepeatMasker");
is_deeply ( [ $rpt->feature1->get_tag_values('Target') ], ['LTR_PGSC0003DMS000000301_448',10681,10775] );
is ($rpt->feature2->seq_id, "LTR_PGSC0003DMS000000301_448");
is ($rpt->feature2->start, 10681);
is ($rpt->feature2->end, 10775);
is ($rpt->feature2->strand, -1);
is ($rpt->feature1->primary_tag, "LTR");
is ($rpt->feature1->source_tag, "RepeatMasker");
is_deeply ([$rpt->feature2->get_tag_values('Target')],['SL2.30ch10',38849,38940]);
}
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