Bio::OntologyIO soflat
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
soflat - a parser for the Sequence Ontology flat-file format
Package variables
No package variables defined.
Included modules
Bio::Ontology::TermFactory
Bio::OntologyIO::dagflat
Inherit
Bio::OntologyIO::dagflat
Synopsis
  use Bio::OntologyIO;

  # 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 $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
Description
Needs Graph.pm from CPAN.
This is essentially a very thin derivation of the dagflat base-parser.
Methods
_initialize
No description
Code
Methods description
None available.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ($self, @args) = @_;
    
    $self->SUPER::_initialize( @args );

    # default term object factory
    $self->term_factory(Bio::Ontology::TermFactory->new(
					  -type => "Bio::Ontology::GOterm"))
	unless $self->term_factory();

} # _initialize
}
General documentation
FEEDBACKTop
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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 lists Your participation is much appreciated.
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Reporting BugsTop
report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
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AUTHORTop
Christian M. Zmasek
Email: czmasek@gnf.org or cmzmasek@yahoo.com
WWW: http://www.genetics.wustl.edu/eddy/people/zmasek/
Address: 
  Genomics Institute of the Novartis Research Foundation
  10675 John Jay Hopkins Drive
  San Diego, CA 92121
CONTRIBUTORTop
 Hilmar Lapp, hlapp at gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
newTop
 Title   : new
 Usage   : $parser = Bio::OntologyIO->new(
                             -format => "soflat",
                             -files => ["/path/to/sofa.ontology"] );
 Function: Creates a new soflat parser.
 Returns : A new soflat parser object, implementing Bio::OntologyIO.
 Args    : -defs_file  => the name of the file holding the term
                          definitions
           -files      => a single ontology flat file holding the
                          term relationships, or an array ref holding
                          the file names
           -file       => if there is only a single flat file, it may
                          also be specified via the -file parameter
           -ontology_name => the name of the ontology; if not specified the
                          parser will auto-discover it by using the term
                          that starts with a '$', and converting underscores
                          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.