Provided by: libbio-perl-perl_1.7.2-2_all
Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats
use Bio::OntologyIO; # do not use directly -- use via Bio::OntologyIO # e.g., the GO parser is a simple extension of this class my $parser = Bio::OntologyIO->new ( -format => "go", -defs_file => "/home/czmasek/GO/GO.defs", -files => ["/home/czmasek/GO/component.ontology", "/home/czmasek/GO/function.ontology", "/home/czmasek/GO/process.ontology"] ); my $go_ontology = $parser->next_ontology(); my $IS_A = Bio::Ontology::RelationshipType->get_instance( "IS_A" ); my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" ); my $RELATED_TO = Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );
Needs Graph.pm from CPAN.
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Christian M. Zmasek Email: czmasek-at-burnham.org or firstname.lastname@example.org WWW: http://monochrome-effect.net/ Address: Genomics Institute of the Novartis Research Foundation 10675 John Jay Hopkins Drive San Diego, CA 92121 CONTRIBUTOR Hilmar Lapp, hlapp at gmx.net
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : $parser = Bio::OntologyIO->new( -format => "go", -defs_file => "/path/to/GO.defs", -files => ["/path/to/component.ontology", "/path/to/function.ontology", "/path/to/process.ontology"] ); Function: Creates a new dagflat parser. Returns : A new dagflat parser object, implementing Bio::OntologyIO. Args : -defs_file => the name of the file holding the term definitions -files => a single ontology flat file holding the term relationships, or an array ref holding the file names (for GO, there will usually be 3 files: component.ontology, function.ontology, process.ontology) -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 to spaces -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. ontology_name 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) parse 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 : next_ontology 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 undef if there is no more ontology in the input. Args : defs_file Title : defs_file Usage : $parser->defs_file( "GO.defs" ); Function: Set/get for the term definitions filename. Returns : The term definitions file name [string]. Args : On set, the term definitions file name [string] (optional). close 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 _flat_files Title : _flat_files Usage : $files_to_parse = $parser->_flat_files(); Function: Get the array of ontology flat files that need to be parsed. Note that this array will decrease in elements over the parsing process. Therefore, it\'s value outside of this module will be limited. Also, be careful not to alter the array unless you know what you are doing. Returns : a reference to an array of zero or more strings Args : none _defs_io Title : _defs_io Usage : $obj->_defs_io($newval) Function: Get/set the Bio::Root::IO instance representing the definition file, if provided (see defs_file()). Example : Returns : value of _defs_io (a Bio::Root::IO object) Args : on set, new value (a Bio::Root::IO object or undef, optional)