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# -*-Perl-*- Test Harness script for Bioperl
# $Id: ClusterIO.t 16089 2009-09-15 21:34:07Z cjfields $
use strict;
BEGIN {
use lib '.';
use Bio::Root::Test;
test_begin(-tests => 12,
-requires_module => 'Time::HiRes');
use_ok('Bio::ClusterIO');
use_ok('Bio::Cluster::ClusterFactory');
}
SKIP: {
test_skip(-tests => 8, -requires_module => 'XML::SAX');
my ($clusterio, $result,$hit,$hsp);
$clusterio = Bio::ClusterIO->new('-tempfile' => 0,
'-format' => 'dbsnp',
'-file' => test_input_file('LittleChrY.dbsnp.xml'));
$result = $clusterio->next_cluster;
ok($result);
is($result->observed, 'C/T');
is($result->type, 'notwithdrawn');
ok($result->seq_5);
ok($result->seq_3);
my @ss = $result->each_subsnp;
is scalar @ss, 5;
is($ss[0]->handle, 'CGAP-GAI');
is($ss[1]->handle, 'LEE');
# don't know if these were ever meant to work... cjf 3/7/07
#is($result->heterozygous, 0.208738461136818);
#is($result->heterozygous_SE, 0.0260274689436777);
}
###################################
# ClusterFactory tests #
###################################
my $fact = Bio::Cluster::ClusterFactory->new();
# auto-recognize implementation class
my $clu = $fact->create_object(-display_id => 'Hs.2');
isa_ok($clu, "Bio::Cluster::UniGeneI");
$clu = $fact->create_object(-namespace => "UNIGENE");
isa_ok($clu, "Bio::Cluster::UniGeneI");
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