Bio::OntologyIO goflat
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Summary
Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format
Package variables
No package variables defined.
Included modules
Bio::Ontology::TermFactory
Inherit
Bio::OntologyIO::dagflat
Synopsis
  use Bio::OntologyIO;
# do not use directly -- use via Bio::OntologyIO 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 $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );
Description
Needs Graph.pm from CPAN.
This is essentially a very thin derivation of the dagflat parser.
Methods
_initialize
No description
Code
Methods description
None available.
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ($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
1;
}
General documentation
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User feedback is an integral part of the evolution of this and other
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Support Top
Please direct usage questions or support issues to the mailing list:
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rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORTop
Christian M. Zmasek
Email: czmasek-at-burnham.org or cmzmasek@yahoo.com
WWW: http://monochrome-effect.net/
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 => "go",
-defs_file => "/path/to/GO.defs",
-files => ["/path/to/component.ontology",
"/path/to/function.ontology",
"/path/to/process.ontology"] );
Function: Creates a new goflat parser.
Returns : A new goflat 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.