1# -*-Perl-*- Test Harness script for Bioperl 2# $Id$ 3 4use strict; 5 6BEGIN { 7 use lib '.'; 8 use Bio::Root::Test; 9 10 test_begin(-tests => 12, 11 -requires_module => 'Time::HiRes'); 12 13 use_ok('Bio::ClusterIO'); 14 use_ok('Bio::Cluster::ClusterFactory'); 15} 16 17SKIP: { 18 test_skip(-tests => 8, -requires_module => 'XML::SAX'); 19 20 my ($clusterio, $result,$hit,$hsp); 21 $clusterio = Bio::ClusterIO->new('-tempfile' => 0, 22 '-format' => 'dbsnp', 23 '-file' => test_input_file('LittleChrY.dbsnp.xml')); 24 25 $result = $clusterio->next_cluster; 26 ok($result); 27 is($result->observed, 'C/T'); 28 is($result->type, 'notwithdrawn'); 29 ok($result->seq_5); 30 ok($result->seq_3); 31 my @ss = $result->each_subsnp; 32 is scalar @ss, 5; 33 is($ss[0]->handle, 'CGAP-GAI'); 34 is($ss[1]->handle, 'LEE'); 35 36 # don't know if these were ever meant to work... cjf 3/7/07 37 #is($result->heterozygous, 0.208738461136818); 38 #is($result->heterozygous_SE, 0.0260274689436777); 39} 40 41################################### 42# ClusterFactory tests # 43################################### 44 45my $fact = Bio::Cluster::ClusterFactory->new(); 46# auto-recognize implementation class 47my $clu = $fact->create_object(-display_id => 'Hs.2'); 48isa_ok($clu, "Bio::Cluster::UniGeneI"); 49$clu = $fact->create_object(-namespace => "UNIGENE"); 50isa_ok($clu, "Bio::Cluster::UniGeneI"); 51