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Bio::OntologyIO::soflaUser Contributed Perl DocumentBio::OntologyIO::soflat(3)

NAME
       Bio::OntologyIO::soflat - a parser for the Sequence Ontology flat-file
       format

SYNOPSIS
	 use Bio::OntologyIO;

	 # do not use directly -- use via Bio::OntologyIO
	 my $parser = Bio::OntologyIO->new
	       ( -format       => "so",	# or soflat
	    -defs_file	  => "/home/czmasek/SO/SO.defs",
		 -file	       => "/home/czmasek/SO/sofa.ontology" );

	 my $sofa_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 base-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

   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 => "soflat",
				    -files => ["/path/to/sofa.ontology"] );
	Function: Creates a new	soflat parser.
	Returns	: A new	soflat 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
		  -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::Ontology::OntologyI.

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX

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