Bio::F...actoryI(3pm)

💖 Bio::Factory::SeqAnalysisParserFactoryI(3pm) — user contributed Perl documentation, bestie 💖

okay so real talk, this is Bio::Factory::SeqAnalysisParserFactoryI, one of the user-contributed Perl docs, and she is a whole interface. like, not a doer, a vibes contract. she describes objects that are capable of creating SeqAnalysisParserI compliant parsers. the blueprint of the blueprint. iconic behavior only. 🎀

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✨ NAME ✨

Bio::Factory::SeqAnalysisParserFactoryI — an interface describing objects capable of creating SeqAnalysisParserI compliant parsers 🦋

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🌸 SYNOPSIS 🌸

    # initialize an object implementing this interface, e.g.
    $factory = Bio::Factory::SeqAnalysisParserFactory->new();
    # obtain a parser object
    $parser = $factory->get_parser(-input=>$inputobj,
                                   -params=>[@params],
                                   -method => $method);
    # $parser is an object implementing Bio::SeqAnalysisParserI
    # annotate sequence with features produced by parser
    while(my $feat = $parser->next_feature()) {
        $seq->add_SeqFeature($feat);
    }

like yes bestie, that's the whole flow: spin up a factory, ask it for a parser, then loop over next_feature() and slam those features onto your sequence with add_SeqFeature(). no cap, that's the loop. 💅

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💜 DESCRIPTION 💜

This is an interface for factory classes capable of instantiating SeqAnalysisParserI implementing parsers. so like, the factory classes are the ones doing the actual work — this is just the promise they're making. ✨

The concept behind the interface is a generic analysis result parsing in high-throughput automated sequence annotation pipelines. that's the whole dream: pipelines, automatic, no human hand-holding, just parsers parsing analysis results and features falling out the other end. If you want more documentation of this concept, go see Bio::SeqAnalysisParserI. 🌈

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🫶 FEEDBACK 🫶

Mailing Lists 💌

User feedback is an integral part of the evolution of this and other Bioperl modules. like, genuinely, your thoughts matter to her. Send your comments and suggestions preferably to one of 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. this is the way. 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 — the more detail you give, the faster someone can slay your bug. 💪

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

bestie please actually report the bug instead of just screaming into the void, she cannot fix what she cannot see 😭

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👑 AUTHOR — Hilmar Lapp, Jason Stajich 👑

Email Hilmar Lapp <hlapp@gmx.net>, Jason Stajich <jason@bioperl.org>

two legends, one module, main character energy for days ⭐

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💀 APPENDIX 💀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — that underscore is the "do not touch, she's internal" signal, iykyk. 🙈

get_parser 🌟

• Title : get_parser
• Usage :

$factory->get_parser(-input=>$inputobj,
                     [ -params=>[@params] ],
                     -method => $method)

• Function: Creates and returns a parser object for the given input and method. The type of input which is suitable depends on the implementation, but a good-style implementation should allow both file names and streams (filehandles).

A particular implementation may not be able to create a parser for the requested method. In this case it shall return undef.

Parameters (-params argument) are passed on to the parser object and therefore are specific to the parser to be created. An implementation of this interface should make this argument optional.

• Example :
• Returns : A Bio::SeqAnalysisParserI implementing object.
• Args : input — object/file where analysis results are coming from, params — parameter to use when parsing/running analysis, method — method of analysis

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and that's the whole page, bestie. go build your factory, make her proud. 🍓

perl v5.32.1 · 2021-08-15 · Bio::F...actoryI(3pm) — mwah, kiss kiss, that's the version, the date, and the manual name, all tucked in like a little bow 🎀💖✨