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

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

🌸 Bio::OntologyIO::dagflat — a base class parser for GO flat-file type formats 💅

okay bestie, so this page is Bio::O...agflat(3pm) from the User Contributed Perl Documentation collection, and no cap, it's the little parser base class that makes GO flat files make sense. Let's get into it. ✨

💖 NAME

Bio::OntologyIO::dagflat — it's giving base class parser for GO flat-file type formats. periodt.

🎀 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" );

lowkey the move here is: don't touch this class directly, use it through Bio::OntologyIO (the GO parser is literally just a lil extension of it). 🦋

✨ DESCRIPTION

It needs Graph.pm from CPAN. That's the whole vibe. Go install it. 🫶

💌 FEEDBACK

📬 Mailing Lists

Bestie, user feedback is an integral part of the evolution of this and every other Bioperl module. Send your comments and suggestions preferably to the Bioperl mailing lists — your participation is much appreciated, fr fr.

  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. (yes, "reponsive" is what the original says, we don't gatekeep typos 💀)

🐛 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

  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: (none, it's empty)
  • 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: (none)

⭐ next_ontology

  • Title: next_ontology
  • Usage: (none)
  • Function: Get the next available ontology from the parser. This is the method prescribed by Bio::OntologyIO.
  • Example: (none)
  • Returns: An object implementing Bio::Ontology::OntologyI, and undef if there is no more ontology in the input.
  • Args: (none)

💜 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: (none)
  • 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: (none)
  • 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, its value outside of this module will be limited. Also, be careful not to alter the array unless you know what you are doing.

⚠️ okay so that "careful not to alter the array" bit? that's not a joke. don't poke the array. 🫣
  • 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: (none)
  • Returns: value of _defs_io (a Bio::Root::IO object)
  • Args: on set, new value (a Bio::Root::IO object or undef, optional)

and that's the whole page, bestie 💖 this one came from perl v5.32.1, dated 2021-08-15, in the Bio::O...agflat(3pm) slot of the manual. go forth and parse those ontologies, you icon. 🌸👑

📦 where this page comes from