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

💖 Bio::OntologyIO::soflat 💖

okay bestie, welcome to the manual page for Bio::OntologyIO::soflat, a lil module that ships inside the User Contributed Perl Documentation collection. she's a parser. she parses Sequence Ontology flat files. she's lowkey iconic and highkey specific. let's get into it 🦋

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✨ NAME ✨

Bio::OntologyIO::soflat — a parser for the Sequence Ontology flat-file format. that's it, that's the whole job description, and she does it well 💅

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🌸 SYNOPSIS 🌸

okay so here's how you actually touch her:

use Bio::OntologyIO;

# do not use directly -- use via Bio::OntologyIO
my $parser = Bio::OntologyIO->new
      ( -format       => "so", # or soflat
   -defs_file    => "/home/czmasek/SO/SO.defs",
        -file         => "/home/czmasek/SO/sofa.ontology" );

my $sofa_ontology = $parser->next_ontology();

my $IS_A    = Bio::Ontology::RelationshipType->get_instance( "IS_A" );
my $PART_OF = Bio::Ontology::RelationshipType->get_instance( "PART_OF" );

bestie, hear me: do not use directly. go through Bio::OntologyIO. that's not a suggestion, that's literally a comment in the source. respect the comment 🫶

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🌈 DESCRIPTION 🌈

okay so two things you gotta know, and I'm gonna say both of them, no cap:

• she needs Graph.pm from CPAN. like, actually needs it. not optional.
• she is essentially a very thin derivation of the dagflat base-parser. that's the whole personality. thin. derived. slaying quietly 🎀

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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. (yes, that's genuinely how much they want to hear from you, it's giving "we're begging, affectionately" 😭)

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🫂 Support

okay so if you have usage questions or support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

...rather than going straight to the module maintainer. the reason is actually good: many experienced and responsive experts will be able to look at the problem and quickly address it. so like, group chat > DM, always 💜

and please include a thorough description of the problem with code and data examples if at all possible. the more context you give, the faster someone can help you. fr fr.

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

https://github.com/bioperl/bioperl-live/issues

go off, file that issue, it's the responsible main character move ⭐

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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 => "soflat",
                            -files => ["/path/to/sofa.ontology"] );

• Function: Creates a new soflat parser. fresh parser, new vibe, zero baggage 💅
• Returns : A new soflat 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
  • -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::Ontology::OntologyI.

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and that's the whole page bestie, you read it, you understood it, you're basically a bioinformatics girlie now 🎀🦋

perl v5.32.1 · 2021-08-15 · Bio::O...:soflat(3pm) — mwah, that's the version, the date, and the page name all wrapped up in a little sign-off bow. take care of her, she's doing her best 💖✨