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Bio::OntologyIO::goflat.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
NAME
Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file formatSYNOPSIS
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.
FEEDBACK
Mailing Lists
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.bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Reporting Bugs
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:http://bugzilla.open-bio.org/
AUTHOR
Christian M. ZmasekEmail: 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
CONTRIBUTOR
Hilmar Lapp, hlapp at gmx.net
APPENDIX
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 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.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre