t/SeqIO/bsml_sax.t

   1 # -*-Perl-*- Test Harness script for Bioperl
   2 # $Id$
   3
   4 use strict;
   5
   6 BEGIN {
   7         use Bio::Root::Test;
   8
   9         test_begin(-tests => 15,
  10                            -requires_modules => [qw(XML::SAX
  11                                                                             XML::SAX::Writer
  12                                                                             XML::SAX::PurePerl
  13                                                                                 XML::SAX::Base)]);
  14
  15         use_ok('Bio::SeqIO');
  16 }
  17
  18 my $verbose = test_debug();
  19
  20 # Using lax parser XML::SAX::PurePerl due to external DTD error (404 for URL,
  21 # invalid redeclaration of predefined entity) instead of others such as
  22 # XML::LibXML::SAX. See GH#376.
  23 local $XML::SAX::ParserPackage = 'XML::SAX::PurePerl';
  24 my $str = Bio::SeqIO->new(-format => 'bsml_sax',
  25                           -verbose => $verbose,
  26                           -file => test_input_file('U83300.bsml'));
  27 my $seq = $str->next_seq;
  28 isa_ok($seq, 'Bio::Seq::RichSeqI');
  29 my @refs = $seq->annotation->get_Annotations('reference');
  30 is(@refs, 2);
  31 is($seq->display_id,'MIVN83300');
  32 is($seq->molecule ,'dna');
  33 ok(! $seq->is_circular);
  34 is($seq->get_dates,2);
  35 is($seq->accession_number, 'U83300');
  36 is($seq->seq_version,1);
  37 my @feats = $seq->get_SeqFeatures;
  38 is(@feats, 2);
  39 is($feats[1]->start, 1);
  40 is($feats[1]->end, 946);
  41 is($feats[1]->get_tag_values('db_xref'), 3);
  42 is($seq->annotation->get_Annotations('reference'),2);
  43 is($seq->annotation->get_Annotations('dblink'),2);