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use lib 't';
use strict;
use warnings;
use Bio::EnsEMBL::Utils::SeqDumper;
use TestUtils qw ( debug test_getter_setter );
use MultiTestDB;
BEGIN { $| = 1;
use Test;
plan tests => 7;
}
our $verbose = 0;
my $multi = MultiTestDB->new();
my $db = $multi->get_DBAdaptor( "core" );
my $seq_dumper = Bio::EnsEMBL::Utils::SeqDumper->new();
ok(ref($seq_dumper) && $seq_dumper->isa('Bio::EnsEMBL::Utils::SeqDumper'));
my $file;
if($verbose) {
$file = undef;
} else {
$file = '/dev/null';
}
#do not dump snps they are not in core db
$seq_dumper->disable_feature_type('variation');
my $slice_adaptor = $db->get_SliceAdaptor();
my $slice =
$slice_adaptor->fetch_by_region('contig', 'AL031658.11.1.162976');
$seq_dumper->dump($slice, 'EMBL', $file);
ok(1);
$seq_dumper->dump($slice, 'GENBANK', $file);
ok(1);
$seq_dumper->dump($slice, 'FASTA', $file);
ok(1);
$slice =
$slice_adaptor->fetch_by_region('chromosome', '20', 30_500_000, 30_600_000);
$seq_dumper->dump($slice, 'EMBL', $file);
ok(1);
$seq_dumper->dump($slice, 'GENBANK', $file);
ok(1);
$seq_dumper->dump($slice, 'FASTA', $file);
ok(1);