/usr/share/perl5/GO/Parsers/obj_emitter.pm is in libgo-perl 0.15-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
package GO::Parsers::obj_emitter;
=head1 NAME
GO::Parsers::obj_emitter - Private class
=head1 SYNOPSIS
do not use this class directly; use GO::Parser
=head1 DESCRIPTION
This is not a file parser - it takes a L<GO::Model::Graph> object as
inputs and fires OBO XML events
=cut
use Exporter;
use base qw(GO::Parsers::base_parser);
use GO::Parsers::ParserEventNames;
use GO::Model::Graph;
use Carp;
use FileHandle;
use strict;
our @TAGS =
qw(id
name
alt_id*
namespace
comment
def
subset*
is_a*
relationship*
is_root
is_obsolete
is_transitive
synonym*
xref_analog*
xref_unknown*
);
sub dtd {
'obo-parser-events.dtd';
}
sub emit_graph {
my ($self, $g) = @_;
$self->start_event(OBO);
$self->fire_source_event($self->file || "object");
$self->start_event(HEADER);
$self->end_event(HEADER);
$g->iterate(sub {
my $ni = shift;
$self->emit_term($ni->term, $g);
return;
});
$self->end_event(OBO);
}
sub emit_term {
my ($self, $t, $g) = @_;
my $stanza = TERM;
if ($t->is_relationship_type) {
$stanza = TYPEDEF;
}
$self->start_event($stanza);
my $parent_rels = $g->get_parent_relationships($t->acc);
foreach my $xtag (@TAGS) {
my $multiple = 0;
my $tag = $xtag;
if ($xtag =~ /(.*)\*$/) {
$tag = $1;
$multiple = 1;
}
if ($tag eq ID) {
$self->event(ID, $t->acc);
}
elsif ($tag eq IS_ROOT) {
$self->event(IS_ROOT, 1)
unless @$parent_rels;
}
elsif ($tag eq IS_OBSOLETE) {
$self->event(IS_OBSOLETE, 1)
if $t->is_obsolete;
}
elsif ($tag eq IS_TRANSITIVE ||
$tag eq IS_SYMMETRIC ||
$tag eq IS_ANTI_SYMMETRIC ||
$tag eq IS_REFLEXIVE ||
$tag eq INVERSE_OF) {
# obo extensions - not dealt with yet
}
elsif ($tag eq XREF_ANALOG || $tag eq XREF_UNKNOWN) {
$self->event($tag=>dbxref($_))
foreach @{$t->dbxref_list || []};
}
elsif ($tag eq DEF) {
my $xrefs = $t->definition_dbxref_list || [];
$self->event(DEF,
[[DEFSTR, $t->definition],
map {
[DBXREF,dbxref($_)]
} @$xrefs
]);
}
elsif ($tag eq SYNONYM) {
my $sh = $t->synonyms_by_type_idx || {};
foreach my $type (keys %$sh) {
foreach my $val (@{$sh->{$type} || []}) {
$self->event(SYNONYM,
[['@'=>[[scope=>$type]]],
[SYNONYM_TEXT,$val]]);
}
}
}
elsif ($tag eq IS_A) {
foreach (grep {$_->type eq 'is_a'} @$parent_rels) {
$self->event(IS_A, $_->parent_acc)
}
}
elsif ($tag eq RELATIONSHIP) {
foreach (grep {$_->type ne 'is_a'} @$parent_rels) {
$self->event(RELATIONSHIP,
[[TYPE,$_->type],
[TO,$_->parent_acc]
]);
}
}
else {
if ($multiple) {
my $method = $tag.'_list';
my $vals = $t->$method();
$self->event($tag, $_)
foreach @$vals;
}
else {
if ($t->can($tag)) {
my $v = $t->$tag();
$self->event($tag, $v) if defined $v;
}
else {
warn("no method for: $tag");
}
}
}
}
$self->end_event($stanza);
}
sub dbxref {
my $xref = shift || confess;
my $name = $xref->name;
return
[[acc=>$xref->acc],
[dbname=>$xref->dbname],
$name ? [name=>$xref->name] : ()
];
}
1;
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