GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
Bio::OntologyIO::goflat(3) User Contributed Perl Documentation Bio::OntologyIO::goflat(3)
 

Bio::OntologyIO::goflat - a parser for the Gene Ontology flat-file format

  use Bio::OntologyIO;
  # do not use directly -- use via Bio::OntologyIO
  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" );

Needs Graph.pm from CPAN.
This is essentially a very thin derivation of the dagflat parser.

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 goflat parser.
 Returns : A new goflat 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.
2019-01-01 perl v5.28.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.