1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
|
#!/usr/local/bin/perl -w
use lib '.';
BEGIN {
eval { require Test; };
use Test;
plan tests => 5;
}
# All tests must be run from the software directory;
# make sure we are getting the modules from here:
use strict;
use GO::Parser;
# ----- REQUIREMENTS -----
# ------------------------
my $parser = new GO::Parser ({format=>'go_ont',
handler=>'obj'});
#$parser->handler->add_root;
ok(1);
$parser->parse (shift @ARGV || "./t/data/generic.0208");
my $a2n = $parser->acc2name_h;
#$parser->parse (shift @ARGV || "./t/data/go-truncated.obo");
$parser = new GO::Parser ({format=>'go_assoc',
handler=>$parser->handler});
$parser->acc2name_h($a2n);
$parser->cache_errors;
$parser->parse (shift @ARGV || "./t/data/test-gene_association.fb");
# we expect one error because of the deliberately bogus last line
# refering to a non-existent GO ID
my @errs = $parser->errlist;
#print $_->sxpr foreach @errs;
ok(@errs == 1); # bogus last line
my $graph = $parser->handler->graph;
my $it = $graph->create_iterator;
while(my $node = $it->next_node_instance){
my $term = $node->term;
#use Data::Dumper;
#print Dumper $graph;
printf "TERM: %s %s\n", $term->acc, $term->name;
die $term->acc unless $term->namespace || $term->is_relationship_type;
my $aspect = $term->get_code_from_namespace;
die $term->acc unless ($term->is_relationship_type || $term->namespace =~ /Gene/ || $aspect eq 'F' || $aspect eq 'C' || $aspect eq 'P');
my $assocs = $term->association_list;
foreach my $assoc (@$assocs) {
my $prod =
$assoc->gene_product;
printf " PROD: %s\n", $prod->symbol;
die unless $assoc->assigned_by eq 'FB';
die unless $assoc->assocdate eq '20040228';
die unless $prod->species->ncbi_taxa_id eq '7227';
}
#this causes an error
my $deep_assocs =
$graph->deep_association_list($term->public_acc);
printf " *DEEP: %d\n", scalar(@$deep_assocs);
}
my $term = $graph->get_term('GO:0003673');
ok(!@{$term->association_list || []});
printf "annots: %d\n", scalar @{$graph->deep_association_list('GO:0003673')};
ok(@{$graph->deep_association_list('GO:0003673')} == 86);
#ok(@{$term->deep_association_list} == 86);
my $prods = $graph->deep_product_list($term->acc);
ok((grep {printf "Type:%s\n", $_->type;$_->type eq 'gene'} @$prods) == 16);
|
