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# -*-Perl-*- Test Harness script for Bioperl
# $Id: interpro.t 15112 2008-12-08 18:12:38Z sendu $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 20,
-requires_module => 'XML::DOM::XPath');
use_ok('Bio::SeqIO::interpro');
}
my $verbose = test_debug();
my $t_file = test_input_file('test.interpro');
my $a_in = Bio::SeqIO->new( -file => $t_file,
-verbose => $verbose,
-format => 'interpro');
isa_ok($a_in, 'Bio::SeqIO');
my $seq = $a_in->next_seq();
ok($seq, 'seq obj is defined');
isa_ok($seq, 'Bio::Seq::RichSeq');
is(scalar( $seq->get_SeqFeatures() ), 6, 'right number of SeqFeatures');
my($feat) = $seq->get_SeqFeatures();
isa_ok($feat,'Bio::SeqFeature::Generic');
is($feat->display_name,'Retinoblastoma-associated protein, B-box', 'display_name()');
ok($seq = $a_in->next_seq(), 'seq object is defined');
is(scalar( $seq->get_SeqFeatures() ),40, 'right number of SeqFeatures');
ok(!($seq = $a_in->next_seq()), 'there is no next_seq (correctly)');
# Bug 1908 (enhancement)
$t_file = test_input_file('interpro_ebi.xml');
my $b_in = Bio::SeqIO->new( -file => $t_file,
-verbose => $verbose,
-format => 'interpro');
$seq = $b_in->next_seq();
ok($seq, 'bug 1908');
my @features = $seq->get_SeqFeatures;
is(scalar @features, 2, 'right number of SeqFeatures');
is($features[0]->primary_tag, 'region', 'primary_tag()');
is($features[0]->display_name, 'Protein of unknown function DUF1021', 'display_name()');
is($features[0]->location->end, 78, 'location->end()');
my @dblinks = $features[0]->annotation->get_Annotations('dblink');
is(scalar @dblinks, 3, 'right number of dblinks');
is($dblinks[1]->primary_id, 'IPR009366', 'first primary_id');
is($dblinks[2]->primary_id, 'PF06257.1', 'second primary_id');
my $other_t_file = test_input_file('test.interpro-go.xml');
my $ipr_in = Bio::SeqIO->new( -file => $other_t_file,
-verbose => $verbose,
-format => 'interpro');
$seq = $ipr_in->next_seq();
@features = $seq->get_SeqFeatures;
@dblinks = $features[0]->annotation->get_Annotations('dblink');
is(scalar @dblinks, 4, 'right number of dblinks');
is($dblinks[3]->primary_id, 'GO:0003677', 'primary_id via dblinks');
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