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Bio::OntologyIO::dagflUser)Contributed Perl DocumenBio::OntologyIO::dagflat(3)

NAME
       Bio::OntologyIO::dagflat	- a base class parser for GO flat-file type
       formats

SYNOPSIS
	 use Bio::OntologyIO;

	 # do not use directly -- use via Bio::OntologyIO
	 # e.g., the GO	parser is a simple extension of	this class
	 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" );
	 my $RELATED_TO	= Bio::Ontology::RelationshipType->get_instance( "RELATED_TO" );

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://bioperl.org/wiki/Mailing_lists	- About	the mailing lists

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       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 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:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR
       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

   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	dagflat	parser.
	Returns	: A new	dagflat	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.

   ontology_name
	Title	: ontology_name
	Usage	: $obj->ontology_name($newval)
	Function: Get/set the name of the ontology parsed by this module.
	Example	:
	Returns	: value	of ontology_name (a scalar)
	Args	: on set, new value (a scalar or undef,	optional)

   parse
	Title	: parse()
	Usage	: $parser->parse();
	Function: Parses the files set with "new" or with methods
		  defs_file and	_flat_files.

		  Normally you should not need to call this method as it will
		  be called automatically upon the first call to
		  next_ontology().

	Returns	: [Bio::Ontology::OntologyEngineI]
	Args	:

   next_ontology
	Title	: next_ontology
	Usage	:
	Function: Get the next available ontology from the parser. This	is the
		  method prescribed by Bio::OntologyIO.
	Example	:
	Returns	: An object implementing Bio::Ontology::OntologyI, and undef if
		  there	is no more ontology in the input.
	Args	:

   defs_file
	Title	: defs_file
	Usage	: $parser->defs_file( "GO.defs"	);
	Function: Set/get for the term definitions filename.
	Returns	: The term definitions file name [string].
	Args	: On set, the term definitions file name [string] (optional).

   close
	Title	: close
	Usage	:
	Function: Closes this ontology stream and associated file handles.

		  Clients should call this method especially when they write
		  ontologies.

		  We need to override this here	in order to close the file
		  handle for the term definitions file.

	Example	:
	Returns	: none
	Args	: none

   _flat_files
	Title	: _flat_files
	Usage	: $files_to_parse = $parser->_flat_files();
	Function: Get the array	of ontology flat files that need to be parsed.

		  Note that this array will decrease in	elements over the
		  parsing process. Therefore, it\'s value outside of this
		  module will be limited. Also,	be careful not to alter	the
		  array	unless you know	what you are doing.

	Returns	: a reference to an array of zero or more strings
	Args	: none

   _defs_io
	Title	: _defs_io
	Usage	: $obj->_defs_io($newval)
	Function: Get/set the Bio::Root::IO instance representing the
		  definition file, if provided (see defs_file()).
	Example	:
	Returns	: value	of _defs_io (a Bio::Root::IO object)
	Args	: on set, new value (a Bio::Root::IO object or undef, optional)

perl v5.32.0			  2019-12-07	   Bio::OntologyIO::dagflat(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX

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