/ 
bioperl-1.2
/ Bio::OntologyIO::simpleGOparser

NAME

simpleGOparser - a simple GO parser returning a SimpleGOEngine

SYNOPSIS

  use Bio::Ontology::simpleGOparser;

  my $parser = Bio::Ontology::simpleGOparser->new
	( -go_defs_file_name    => "/home/czmasek/GO/GO.defs",
	  -components_file_name => "/home/czmasek/GO/component.ontology",
	  -functions_file_name  => "/home/czmasek/GO/function.ontology",
	  -processes_file_name  => "/home/czmasek/GO/process.ontology" );

  my $engine = $parser->parse();

  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.

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://bio.perl.org/MailList.html             - 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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

AUTHOR

Christian M. Zmasek

Email: czmasek@gnf.org or cmzmasek@hotmail.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

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::simpleGOparser->new( -go_defs_file_name    => "/path/to/GO.defs",
                                                        -components_file_name => "/path/to/component.ontology"
                                                        -functions_file_name  => "/path/to/function.ontology"
                                                        -processes_file_name  => "/path/to/process.ontology" );                      
Function: Creates a new simpleGOparser.
Returns : A new simpleGOparser object.
Args    : -go_defs_file_name    => the GO defs-file name
          -components_file_name => the component.ontology-file name
          -functions_file_name  => the function.ontology-file name
          -processes_file_name  => the process.ontology-file name

init

Title   : init()
Usage   : $parser->init();   
Function: Initializes this object.
Returns : 
Args    :

parse

Title   : parse()
Usage   : $parser->parse();   
Function: Parses the files set wirh "new" or with methods
          go_defs_file_name, components_file_name, functions_file_name,
          processes_file_name.
Returns : [Bio::Ontology::SimpleGOEngine]
Args    :

go_defs_file_name

Title   : go_defs_file_name
Usage   : $parser->go_defs_file_name( "GO.defs" );
Function: Set/get for the GO defs-file_name.
Returns : The GO defs-file_name [string].
Args    : The GO defs-file_name [string] (optional).

components_file_name

Title   : components_file_name
Usage   : $parser-> components_file_name( "function.ontology" );
Function: Set/get for the function ontology file name.
Returns : The function ontology file name [string].
Args    : The function ontology file name [string] (optional).

functions_file_name

Title   : functions_file_name
Usage   : $parser->functions_file_name( "function.ontology" );
Function: Set/get for functions file name.
Returns : The functions file name [string].
Args    : The functions file name [string] (optional).

processes_file_name

Title   : processes_file_name
Usage   : $parser->processes_file_name( "GO.defs" );
Function: Set/get for the processes file name.
Returns : The processes file name [string].
Args    : The processes file name [string] (optional).