6
test_begin( -tests => 38 );
7
use_ok('Bio::DB::Taxonomy');
8
use_ok('Bio::Tree::Tree');
12
my ($db, $id, @ids, $node, $node2, $ancestor, @children, %common_names, $tree, @descs);
15
# Test Bio::DB::Taxonomy::greengenes
17
ok $db = Bio::DB::Taxonomy->new( -source => 'greengenes' );
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isa_ok $db, 'Bio::DB::Taxonomy::greengenes';
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isa_ok $db, 'Bio::DB::Taxonomy::list';
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isa_ok $db, 'Bio::DB::Taxonomy';
23
ok $db = Bio::DB::Taxonomy->new(
24
-source => 'greengenes',
25
-taxofile => test_input_file('taxonomy', 'greengenes_taxonomy_16S_candiv_gg_2011_1.txt'),
28
@ids = $db->get_taxonid('Homo sapiens');
31
@ids = $db->get_taxonid('s__Bacteroides uniformis');
35
ok $node = $db->get_taxon($id);
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is $node->object_id, $node->id;
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is $node->ncbi_taxid, undef;
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is $node->rank, 'species';
40
is $node->parent_id, 'gg6';
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is $node->node_name, 's__Bacteroides uniformis';
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is $node->scientific_name, $node->node_name;
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is ${$node->name('scientific')}[0], $node->node_name;
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%common_names = map { $_ => 1 } $node->common_names;
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is scalar keys %common_names, 0;
49
is $node->division, undef;
50
is $node->genetic_code, undef;
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is $node->mitochondrial_genetic_code, undef;
53
# briefly test some Bio::Tree::NodeI methods
54
ok $ancestor = $node->ancestor;
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is $ancestor->scientific_name, 'g__Bacteroides';
57
# unless set explicitly, Bio::Taxon doesn't return anything for
58
# each_Descendent; must ask the database directly
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ok @children = $ancestor->db_handle->each_Descendent($ancestor);
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is scalar @children, 2;
62
# do some trickier things...
63
ok $node2 = $db->get_taxon('gg104');
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is $node2->scientific_name, 'o__Synergistales';
66
# briefly check that we can use some Tree methods
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$tree = Bio::Tree::Tree->new();
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is $tree->get_lca($node, $node2)->scientific_name, 'k__Bacteria';
70
# can we actually form a Tree and use other Tree methods?
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ok $tree = Bio::Tree::Tree->new(-node => $node);
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is $tree->number_nodes, 7;
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is $tree->get_nodes, 7;
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is $tree->find_node(-rank => 'genus')->scientific_name, 'g__Bacteroides';
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is $tree->find_node(-rank => 'class')->scientific_name, 'c__Bacteroidia';
77
# check that getting the ancestor still works now we have explitly set the
78
# ancestor by making a Tree
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is $node->ancestor->scientific_name, 'g__Bacteroides';
81
# we can recursively fetch all descendents of a taxon
82
my $lca = $db->get_taxon( -name => 'f__Enterobacteriaceae' );
83
ok @descs = $db->each_Descendent($lca);
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@descs = $db->get_all_Descendents($lca);