| Bio::OntologyIO::dagflat(3pm) | User Contributed Perl Documentation | Bio::OntologyIO::dagflat(3pm) |
Bio::OntologyIO::dagflat - a base class parser for GO flat-file type formats
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" );
Needs Graph.pm from CPAN.
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
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.
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
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
Hilmar Lapp, hlapp at gmx.net
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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.
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)
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 :
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 :
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).
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
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
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)
| 2021-08-15 | perl v5.32.1 |