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use strict;
use Test::Exception;
use Test::More;
use Test::RequiresInternet;
use_ok('Bio::DB::Taxonomy');
my %params;
if (defined $ENV{BIOPERLEMAIL}) {
$params{'-email'} = $ENV{BIOPERLEMAIL};
$params{'-delay'} = 1;
}
{
ok my $db = Bio::DB::Taxonomy->new(-source => 'entrez', %params);
isa_ok $db, 'Bio::DB::Taxonomy::entrez';
isa_ok $db, 'Bio::DB::Taxonomy';
}
{
my $db = Bio::DB::Taxonomy->new(-source => 'entrez', %params);
my $id;
my $n;
cmp_ok $db->get_num_taxa, '>', 880_000; # 886,907 as of 08-May-2012
$id = $db->get_taxonid('Homo sapiens');
is $id, 9606;
# easy test on human, try out the main Taxon methods
ok $n = $db->get_taxon(9606);
is $n->id, 9606;
is $n->object_id, $n->id;
is $n->ncbi_taxid, $n->id;
is $n->parent_id, 9605;
is $n->rank, 'species';
is $n->node_name, 'Homo sapiens';
is $n->scientific_name, $n->node_name;
is ${$n->name('scientific')}[0], $n->node_name;
my %common_names = map { $_ => 1 } $n->common_names;
cmp_ok keys %common_names, '>=', 3, ref($db).": common names";
ok exists $common_names{human};
is $n->division, 'Primates';
is $n->genetic_code, 1;
is $n->mitochondrial_genetic_code, 2;
ok defined $n->pub_date;
ok defined $n->create_date;
ok defined $n->update_date;
# briefly test some Bio::Tree::NodeI methods
ok my $ancestor = $n->ancestor;
is $ancestor->scientific_name, 'Homo';
# unless set explicitly, Bio::Taxon doesn't return anything for
# each_Descendent; must ask the database directly
ok my @children = $ancestor->db_handle->each_Descendent($ancestor);
cmp_ok @children, '>', 0;
sleep(3);
# do some trickier things...
ok my $n2 = $db->get_Taxonomy_Node('89593');
is $n2->scientific_name, 'Craniata';
# briefly check we can use some Tree methods
my $tree = Bio::Tree::Tree->new();
is $tree->get_lca($n, $n2)->scientific_name, 'Craniata';
# get lineage_nodes
my @nodes = $tree->get_nodes;
is scalar(@nodes), 0;
my @lineage_nodes;
@lineage_nodes = $tree->get_lineage_nodes($n->id); # read ID, only works if nodes have been added to tree
is scalar @lineage_nodes, 0;
@lineage_nodes = $tree->get_lineage_nodes($n); # node object always works
cmp_ok(scalar @lineage_nodes, '>', 20);
# get lineage string
like($tree->get_lineage_string($n), qr/cellular organisms;Eukaryota/);
like($tree->get_lineage_string($n,'-'), qr/cellular organisms-Eukaryota/);
like($tree->get_lineage_string($n2), qr/cellular organisms;Eukaryota/);
# can we actually form a Tree and use other Tree methods?
ok $tree = Bio::Tree::Tree->new(-node => $n);
cmp_ok($tree->number_nodes, '>', 20);
cmp_ok(scalar($tree->get_nodes), '>', 20);
is $tree->find_node(-rank => 'genus')->scientific_name, 'Homo';
# check that getting the ancestor still works now we have explitly set the
# ancestor by making a Tree
is $n->ancestor->scientific_name, 'Homo';
sleep(3);
ok $n = $db->get_Taxonomy_Node('1760');
is $n->scientific_name, 'Actinomycetes';
sleep(3);
# entrez isn't as good at searching as flatfile, so we have to special-case
my @ids = sort $db->get_taxonids('Chloroflexi');
is scalar @ids, 2;
is_deeply \@ids, [200795, 32061];
$id = $db->get_taxonids('Chloroflexi (class)');
is($id, 'No hit');
@ids = $db->get_taxonids('Rhodotorula');
cmp_ok @ids, '>=' , 1;
# From NCBI: Taxid 592558 was merged into taxid 5533 on June 16, 2017
is( (grep { $_ == 592558 } @ids), 0, 'Value no longer found');
ok grep { $_ == 5533 } @ids;
}
# we can recursively fetch all descendents of a taxon
{
my $db = Bio::DB::Taxonomy->new(-source=>"entrez", %params);
$db->get_taxon(10090);
my $lca = $db->get_taxon(314146);
my @descs = $db->get_all_Descendents($lca);
cmp_ok @descs, '>=', 17;
}
# tests for #182
{
my $db = Bio::DB::Taxonomy->new(-source=>"entrez", %params);
my @taxa = qw(viruses Deltavirus unclassified plasmid);
for my $taxon (@taxa) {
test_taxid($db, $taxon);
}
sub test_taxid {
my ($db, $taxa) = @_;
my @taxonids = $db->get_taxonids($taxa);
cmp_ok(scalar(@taxonids), '>', 0, "Got IDs returned for $taxa:".join(',', @taxonids));
my $taxon;
lives_ok { $taxon = $db->get_taxon(-taxonid => pop @taxonids) } "IDs generates a Bio::Taxonomy::Node";
if (defined $taxon) {
like( $taxon->scientific_name, qr/$taxa/i, "Name returned matches $taxa");
} else {
ok(0, "No taxon object returned for $taxa");
}
}
}
# tests for #212
{
my $db = Bio::DB::Taxonomy->new( -source => "entrez", %params);
# String | What I expect | What I get
# ---------------------- | ------------- | ----------
# 'Lissotriton vulgaris' | 8324 | 8324
# 'Chlorella vulgaris' | 3077 | 3077
# 'Phygadeuon solidus' | 1763951 | 1763951
# 'Ovatus' | 666060 | 666060
# 'Phygadeuon ovatus' | 2890685 | 2890685
# 'Zaphod Beeblebrox' | "No hit" | "No hit"
my @ids;
@ids = $db->get_taxonids('Lissotriton vulgaris');
is $ids[0], 8324, 'Correct: Lissotriton vulgaris';
@ids = $db->get_taxonids('Chlorella vulgaris');
is $ids[0], 3077, 'Correct: Chlorella vulgaris';
@ids = $db->get_taxonids('Phygadeuon solidus');
is $ids[0], 1763951, 'Correct: Phygadeuon solidus';
@ids = $db->get_taxonids('Ovatus');
is $ids[0], 666060, 'Correct: Ovatus';
@ids = $db->get_taxonids('Phygadeuon ovatus');
is $ids[0], '2890685', 'Correct: 2890685';
@ids = $db->get_taxonids('Zaphod Beeblebrox');
is $ids[0], 'No hit', 'Correct: No hit';
}
done_testing();
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