| Bio::OntologyIO(3pm) | User Contributed Perl Documentation | Bio::OntologyIO(3pm) |
Bio::OntologyIO - Parser factory for Ontology formats
use Bio::OntologyIO;
my $parser = Bio::OntologyIO->new(-format => "go",
-file=> $file);
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";
}
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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; the following are
presently supported:
goflat: DAG-Edit Gene Ontology flat files
go : synonymous to goflat
soflat: DAG-Edit Sequence Ontology flat files
so : synonymous to soflat
simplehierarchy: text format with one term per line
and indentation giving the hierarchy
evoc : synonymous to simplehierarchy
interpro: InterPro XML
interprosax: InterPro XML - this is actually not a
Bio::OntologyIO compliant parser; instead it
persists terms as they are encountered.
L<Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler>
obo : OBO format style from Gene Ontology Consortium
-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 L<Bio::Ontology::OntologyEngineI> object
to be reused (will be created otherwise); note
that every L<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 : format Usage : $format = $parser->format() Function: Get the ontology format Returns : ontology format Args : none
Title : next_ontology
Usage : $ont = $stream->next_ontology()
Function: Reads the next ontology object from the stream and returns it.
Returns : a L<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
L<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)
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.
Title : _load_format_module Usage : *INTERNAL OntologyIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
| 2021-08-15 | perl v5.32.1 |