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use strict;
use vars qw($NUMTESTS);
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 5);
use_ok('Bio::Tools::Run::Mdust');
use_ok('Bio::SeqIO');
}
my $input = Bio::SeqIO->new( -file => test_input_file('NM_002254.gb'),
-format => 'Genbank' );
my $seq = $input->next_seq;
my $mdust = Bio::Tools::Run::Mdust->new(
-target => $seq,
);
isa_ok $mdust, "Bio::Tools::Run::Mdust";
SKIP: {
test_skip(-requires_executable => $mdust,
-tests => 2);
$mdust->run;
my @excluded = grep { $_->primary_tag eq 'Excluded' } $seq->top_SeqFeatures;
is (scalar(@excluded),3);
my $input2 = Bio::SeqIO->new( -file => test_input_file('NM_002254.tfa'),
-format => 'Fasta');
my $seq2 = $input2->next_seq;
$mdust->coords(0);
my $masked = $mdust->run($seq2);
like $masked->seq, qr/N+/;
}