t/SeqIO/gbxml.t

   1 use strict;
   2
   3 BEGIN {
   4    use lib '.';
   5    use Bio::Root::Test;
   6
   7    test_begin(-tests => 14,
   8               -requires_modules => [ qw(XML::SAX) ]
   9               );
  10
  11    use_ok('Bio::SeqIO::gbxml');
  12 }
  13
  14 my $verbose = test_debug();
  15
  16 my $in = Bio::SeqIO->new(-format  => 'gbxml',
  17                           -verbose => $verbose,
  18                           # This class can't parse dbEST data yet...
  19                           # -file    => test_input_file('roa1.gbxml'));
  20                           # So let's try a <GBSeq> file:
  21                           -file    => test_input_file('EG352462.gbxml'));
  22 isa_ok($in, 'Bio::SeqIO');
  23 my $seq = $in->next_seq();
  24 is($seq->molecule,   'mRNA',                                            'molecule');
  25 is($seq->alphabet,   'dna',                                             'alphabet');
  26 is($seq->primary_id,  116038450,                                        'primary_id');
  27 is($seq->display_id, 'EG352462',                                        'display_id');
  28 is($seq->version,     1,                                                'version');
  29 is($seq->is_circular, 0,                                                'is_circular');
  30
  31 is(substr($seq->description, 0, 10), 'SAAH-aad23',                      'description');
  32 is(substr($seq->seq,         0, 10), 'aataaaatta',                      'sequence');
  33
  34 my @class = $seq->species->classification;
  35 is($class[$#class],'Eukaryota',                                         'classification');
  36
  37 my ($feat) = $seq->get_SeqFeatures;
  38 is_deeply([ $feat->get_tag_values('clone_lib') ], [ 'Agen 0058' ],      'feat - clone_lib');
  39 is_deeply([ $feat->get_tag_values('db_xref') ],   [ 'taxon:79327' ],    'feat - db_xref');
  40 is_deeply([ $feat->get_tag_values('lab_host') ],  [ 'DH10B cells' ],    'feat - lab_host');
  41
  42
  43