Bio::O...:goflat(3pm)

✨ NAME ✨

Bio::OntologyIO::goflat — it's a parser for the Gene Ontology flat-file format, bestie 💖

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🌸 SYNOPSIS 🌸

  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" );

okay so note the little comment in there: do not use directly — use via Bio::OntologyIO. That's not a suggestion, that's the vibe. 🫶

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🦋 DESCRIPTION 🦋

Needs Graph.pm from CPAN. Like, it genuinely needs it, go get it. 📦

Otherwise? It's essentially a very thin derivation of the dagflat parser. That's the whole tea — thin derivation, dagflat energy, but make it GO. ✨

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💬 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.

bestie please include code AND data examples, the experts eat that up 💅

🐛 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

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👑 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

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk 🔍

🎀 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 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.

Let's break that arg list down, because it's a lot and you deserve clarity 🧚

• -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, you can also pass it through this parameter instead.
• -ontology_name — the name of the ontology. If you don't specify it, the parser auto-discovers it by using the term that starts with a $, and converting underscores to spaces. no cap ✨
• -engine — the Bio::Ontology::OntologyEngineI object to be reused (it will be created otherwise). Note that every Bio::Ontology::OntologyI will qualify as well, since that one inherits from the former. 👑

See Bio::OntologyIO.

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and that's the whole page, bestie!! 💖✨ this beauty is from the User Contributed Perl Documentation, shipping with perl v5.32.1, dated 2021-08-15 — slay, iconic, periodt. 🎀🦋🌸💅