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use strict;
BEGIN {
use Bio::Root::Test;
test_begin(-tests => 14,
-requires_modules => [ qw(XML::SAX) ]
);
use_ok('Bio::SeqIO::gbxml');
}
my $verbose = test_debug();
my $in = Bio::SeqIO->new(-format => 'gbxml',
-verbose => $verbose,
# This class can't parse dbEST data yet...
# -file => test_input_file('roa1.gbxml'));
# So let's try a <GBSeq> file:
-file => test_input_file('EG352462.gbxml'));
isa_ok($in, 'Bio::SeqIO');
my $seq = $in->next_seq();
is($seq->molecule, 'mRNA', 'molecule');
is($seq->alphabet, 'dna', 'alphabet');
is($seq->primary_id, 116038450, 'primary_id');
is($seq->display_id, 'EG352462', 'display_id');
is($seq->version, 1, 'version');
is($seq->is_circular, 0, 'is_circular');
is(substr($seq->description, 0, 10), 'SAAH-aad23', 'description');
is(substr($seq->seq, 0, 10), 'aataaaatta', 'sequence');
my @class = $seq->species->classification;
is($class[$#class],'Eukaryota', 'classification');
my ($feat) = $seq->get_SeqFeatures;
is_deeply([ $feat->get_tag_values('clone_lib') ], [ 'Agen 0058' ], 'feat - clone_lib');
is_deeply([ $feat->get_tag_values('db_xref') ], [ 'taxon:79327' ], 'feat - db_xref');
is_deeply([ $feat->get_tag_values('lab_host') ], [ 'DH10B cells' ], 'feat - lab_host');
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