Bio
OntologyIO
Summary
Bio::OntologyIO - Parser factory for Ontology formats
Package variables
Privates (from "my" definitions)
%format_driver_map = ( "go" => "goflat", "so" => "soflat", "interpro" => "InterProParser", )
Included modules
Inherit
Synopsis
use Bio::OntologyIO;
my $parser = Bio::OntologyIO->new(-format => "go", ...);
while(my $ont = $parser->next_ontology()) {
print "read ontology ",$ont->name()," with ",
scalar($ont->get_root_terms)," root terms, and ",
scalar($ont->get_leaf_terms)," leaf terms\n";
}
Description
This is the parser factory for different ontology sources and
formats. Conceptually, it is very similar to
Bio::SeqIO, but the
difference is that the chunk of data returned as an object is an
entire ontology.
Methods
Methods description
Title : new
Usage : my $parser = Bio::OntologyIO->new(-format => 'go', @args);
Function: Returns a stream of ontologies opened on the specified input
for the specified format.
Returns : An ontology parser (an instance of Bio::OntologyIO) initialized
for the specified format.
Args : Named parameters. Common parameters are
-format - the format of the input; supported right now are
'go' (synonymous with goflat), 'so' (synonymous
with soflat), and 'interpro'
-file - the file holding the data
-fh - the stream providing the data (-file and -fh are
mutually exclusive)
-ontology_name - the name of the ontology
-engine - the Bio::Ontology::OntologyEngineI object
to be reused (will be created otherwise); note
that every Bio::Ontology::OntologyI will
qualify as well since that one inherits from the
former.
-term_factory - the ontology term factory to use. Provide a
value only if you know what you are doing.
DAG-Edit flat file parsers will usually also accept the
following parameters.
-defs_file - the name of the file holding the term
definitions
-files - an array ref holding the file names (for GO,
there will usually be 3 files: component.ontology,
function.ontology, process.ontology)
Other parameters are specific to the parsers. |
Title : next_ontology
Usage : $ont = $stream->next_ontology()
Function: Reads the next ontology object from the stream and returns it.
Returns : a Bio::Ontology::OntologyI compliant object, or undef at the
end of the stream
Args : none |
Title : term_factory
Usage : $obj->term_factory($newval)
Function: Get/set the ontology term factory to use.
As a user of this module it is not necessary to call this
method as there will be default. In order to change the
default, the easiest way is to instantiate
Bio::Ontology::TermFactory with the proper -type
argument. Most if not all parsers will actually use this
very implementation, so even easier than the aforementioned
way is to simply call
$ontio->term_factory->type("Bio::Ontology::MyTerm").
Example :
Returns : value of term_factory (a Bio::Factory::ObjectFactoryI object)
Args : on set, new value (a Bio::Factory::ObjectFactoryI object, optional) |
Title : _load_format_module
Usage : *INTERNAL OntologyIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args : |
Methods code
sub new
{ my ($caller,@args) = @_;
my $class = ref($caller) || $caller;
if( $class =~ /Bio::OntologyIO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param;
my $format = $class->_map_format($param{'-format'});
return undef unless( $class->_load_format_module($format) );
return "Bio::OntologyIO::$format"->new(@args);
}} | sub _initialize
{ my($self, @args) = @_;
my ($eng,$fact,$ontname) =
$self->_rearrange([qw(TERM_FACTORY)
], @args);
$self->term_factory($fact) if $fact;
$self->_initialize_io(@args);} | sub next_ontology
{ shift->throw_not_implemented(); } | sub term_factory
{ my $self = shift;
return $self->{'term_factory'} = shift if @_;
return $self->{'term_factory'};} | sub _load_format_module
{ my ($self, $format) = @_;
my $module = "Bio::OntologyIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END
$self: $format cannot be found
Exception $@
For more information about the OntologyIO system please see the docs.
This includes ways of checking for formats at compile time, not run time
END
}
return $ok;} | sub DESTROY
{ my $self = shift;
$self->close();} | sub _map_format
{ my $self = shift;
my $format = shift;
my $mod;
if($format) {
$mod = $format_driver_map{lc($format)};
$mod = lc($format) unless $mod;
} else {
$self->throw("unable to guess ontology format, specify -format");
}
return $mod;} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://bugzilla.bioperl.org/
Email hlapp at gmx.net
Describe contact details here
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Some of these are actually 'protected' in OO speak, which means you
may or will want to utilize them in a derived ontology parser, but
you should not call them from outside.