[Bioperl-l] Bio::Ontology - parsing GO files

James Mitchell mitchell at odin.mdacc.tmc.edu
Mon Feb 2 16:45:04 EST 2004

I'm using Bio::Ontology modules to access GO tree information, ie.
ancestors/descendants of a given node.  I'm using it like this:
use strict;
use Bio::Ontology::SimpleGOEngine;

my $gendir = $ENV{GeneLink_Dir};
my $deffile = $gendir . "GO.defs";
my $comfile = $gendir . "component.ontology";
my $funfile = $gendir . "function.ontology";
my $profile = $gendir . "process.ontology";
my $parser = Bio::Ontology::SimpleGOEngine->new
	( -defs_file => $deffile,
	  -files     => [$comfile,
	                 $profile] );
my $engine = $parser->parse();
I'm getting this error though:
Can't locate object method "parse" via package
"Bio::Ontology::SimpleGOEngine" (
perhaps you forgot to load "Bio::Ontology::SimpleGOEngine"?)
Is this the correct method for parsing GO files?  I'm using version 1.4 on


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