Bio::S...ParserI(3pm)

💖 NAME 💖

Bio::SeqAnalysisParserI — the sequence analysis output parser interface, bestie. It's the vibe, the blueprint, the whole interface situation. 🧚

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🌸 SYNOPSIS 🌸

okay so picture this, you get yourself a SeqAnalysisParserI somehow, like:

# get a SeqAnalysisParserI somehow, e.g. by
my $parser = Bio::Factory::SeqAnalysisParserFactory->get_parser(
                        '-input' => 'inputfile', '-method' => 'genscan');
while( my $feature = $parser->next_feature() ) {
    print "Feature from ", $feature->start, " to ", $feature->end, "\n";
}

and then you just keep pulling features until there aren't any left. iconic behavior, honestly. ✨

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✨ DESCRIPTION ✨

SeqAnalysisParserI is a generic interface for describing sequence analysis result parsers. and what counts as "sequence analysis" here? it's a search for similarities, or spotting features on the sequence — think a databank search, or a gene prediction result. 🧬

The concept behind this interface is to have a generic interface in sequence annotation pipelines (as used, for example, in high-throughput automated sequence annotation). This interface enables plug-and-play for new analysis methods and their corresponding parsers, without you having to go modify the core of the annotation pipeline. like, no cap. In this concept the annotation pipeline only has to rely on:

• a list of methods whose results it's gonna process, and
• a factory it can ask for the corresponding parser that implements this interface. 🎀

See Bio::Factory::SeqAnalysisParserFactoryI and Bio::Factory::SeqAnalysisParserFactory for the interface and an implementation of the corresponding factory. iykyk.

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🫶 FEEDBACK 🫶

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules — like, literally, it's giving growth. Send your comments and suggestions preferably to one of 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. 🙏 (seriously, the more detail the better — give them the whole lore.)

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 - Hilmar Lapp, Jason Stajich 👑

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

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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 like the secret handshake, don't touch it. 🙈

next_feature

• Title: next_feature
• Usage: $seqfeature = $obj->next_feature();
• Function: Returns the next feature available in the analysis result, or undef if there are no more features.
• Example:
• Returns: A Bio::SeqFeatureI implementing object, or undef if there are no more features.
• Args: none

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okay that's the whole page, you ate that. 🍓 this was perl v5.32.1, dated 2021-08-15 — stay hydrated, keep your features coming, and remember: no more features means undef, not a crisis. periodt. 💖🦋⭐