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Bio::OntologyIO::obo(3User Contributed Perl DocumentatiBio::OntologyIO::obo(3)

NAME
       Bio::OntologyIO::obo - parser for OBO flat-file format

SYNOPSIS
	 use Bio::OntologyIO;

	 # do not use directly -- use via Bio::OntologyIO
	 my $parser = Bio::OntologyIO->new
	       ( -format => "obo",
		 -file	 =>  "gene_ontology.obo");

	 while(my $ont = $parser->next_ontology()) {
	 print "read ontology ",$ont->name()," with ",
		      scalar($ont->get_root_terms), " root terms, and ",
		      scalar($ont->get_all_terms),  " total terms, and ",
		      scalar($ont->get_leaf_terms), " leaf terms\n";
	 }

DESCRIPTION
       Parser for OBO flat-file	format.	'obo' example:

	format-version:	1.2
	ontology: so/dev/externalDerived
	property_value:	owl:versionInfo	"$Revision: 80 $" xsd:string
	default-namespace: SO

	[Term]
	id: SO_0000343
	name: match
	def: "A	region of sequence, aligned to another sequence." []

	[Term]
	id: SO_0000039
	name: match_part
	def: "A	part of	a match." []
	is_a: SO_0000343

       Specification: <http://www.geneontology.org/GO.format.obo-1_2.shtml>.

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
       Sohel Merchant

       Email: s-merchant@northwestern.edu

       Address:

	 Northwestern University
	 Center	for Genetic Medicine (CGM), dictyBase
	 Suite 1206,
	 676 St. Clair st
	 Chicago IL 60611

   CONTRIBUTOR
	Hilmar Lapp, hlapp at gmx.net
	Chris Mungall, cjm at fruitfly.org
	Brian Osborne, briano@bioteam.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 => "obo",
				    -file => "gene_ontology.obo");
	Function: Creates a new	dagflat	parser.
	Returns	: A new	dagflat	parser object, implementing Bio::OntologyIO.
	Args	: -file	     =>	a single ontology flat file holding the
				terms, descriptions and	relationships
		  -ontology_name => the	name of	the ontology; if not specified the
				 parser	will assign the	name of	the ontology as	the
				 default-namespace header value	from the OBO file.
		  -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 nothing if
		  there	is no more ontology in the input.
	Args	:

   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

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX

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