Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file format
No package variables defined.
# do not use directly -- use via Bio::OntologyIO
my $parser = Bio::OntologyIO->new
( -format => "so", # or soflat
-defs_file => "/home/czmasek/SO/SO.defs",
-file => "/home/czmasek/SO/sofa.ontology" );
my $sofa_ontology = $parser->next_ontology();
my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
Needs Graph.pm from CPAN.
This is essentially a very thin derivation of the dagflat base-parser.
my ($self, @args) = @_;
$self->SUPER::_initialize( @args );
-type => "Bio::Ontology::GOterm"))
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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 : $parser = Bio::OntologyIO->new(
-format => "soflat",
-files => ["/path/to/sofa.ontology"] );
Function: Creates a new soflat parser.
Returns : A new soflat parser object, implementing Bio::OntologyIO.
Args : -defs_file => the name of the file holding the term
-files => a single ontology flat file holding the
term relationships, or an array ref holding
the file names
-file => if there is only a single flat file, it may
also be specified via the -file parameter
-ontology_name => the name of the ontology; if not specified the
parser will auto-discover it by using the term
that starts with a $, and converting underscores
-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