| Bio::OntologyIO::obo(3pm) | User Contributed Perl Documentation | Bio::OntologyIO::obo(3pm) |
Bio::OntologyIO::obo - parser for OBO flat-file format
use Bio::OntologyIO;
# do not use directly -- use via Bio::OntologyIO
my $parser = Bio::OntologyIO->new
( -format => "obo",
-file => "gene_ontology.obo");
while(my $ont = $parser->next_ontology()) {
print "read ontology ",$ont->name()," with ",
scalar($ont->get_root_terms), " root terms, and ",
scalar($ont->get_all_terms), " total terms, and ",
scalar($ont->get_leaf_terms), " leaf terms\n";
}
Parser for OBO flat-file format. 'obo' example:
format-version: 1.2 ontology: so/dev/externalDerived property_value: owl:versionInfo "$Revision: 80 $" xsd:string default-namespace: SO [Term] id: SO_0000343 name: match def: "A region of sequence, aligned to another sequence." [] [Term] id: SO_0000039 name: match_part def: "A part of a match." [] is_a: SO_0000343
Specification: <http://www.geneontology.org/GO.format.obo-1_2.shtml>.
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Sohel Merchant
Email: s-merchant@northwestern.edu
Address:
Northwestern University Center for Genetic Medicine (CGM), dictyBase Suite 1206, 676 St. Clair st Chicago IL 60611
Hilmar Lapp, hlapp at gmx.net Chris Mungall, cjm at fruitfly.org Brian Osborne, briano@bioteam.net
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : $parser = Bio::OntologyIO->new(
-format => "obo",
-file => "gene_ontology.obo");
Function: Creates a new dagflat parser.
Returns : A new dagflat parser object, implementing Bio::OntologyIO.
Args : -file => a single ontology flat file holding the
terms, descriptions and relationships
-ontology_name => the name of the ontology; if not specified the
parser will assign the name of the ontology as the
default-namespace header value from the OBO file.
-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.
See Bio::OntologyIO.
Title : ontology_name Usage : $obj->ontology_name($newval) Function: Get/set the name of the ontology parsed by this module. Example : Returns : value of ontology_name (a scalar) Args : on set, new value (a scalar or undef, optional)
Title : parse()
Usage : $parser->parse();
Function: Parses the files set with "new" or with methods
defs_file and _flat_files.
Normally you should not need to call this method as it will
be called automatically upon the first call to
next_ontology().
Returns : Bio::Ontology::OntologyEngineI
Args :
Title : next_ontology
Usage :
Function: Get the next available ontology from the parser. This is the
method prescribed by Bio::OntologyIO.
Example :
Returns : An object implementing Bio::Ontology::OntologyI, and nothing if
there is no more ontology in the input.
Args :
Title : close
Usage :
Function: Closes this ontology stream and associated file handles.
Clients should call this method especially when they write
ontologies.
We need to override this here in order to close the file
handle for the term definitions file.
Example :
Returns : none
Args : none
| 2020-10-28 | perl v5.30.3 |