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BioPerl-1.7.8
River stage two • 60 direct dependents • 64 total dependents
/ Bio::OntologyIO::dagflat

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)