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

💖 Bio::S...ctionI — the tea on the interface for a whole lil squad of SeqFeatureI objects 💖

okay bestie, welcome to the Bio::SeqFeature::CollectionI page, part of the User Contributed Perl Documentation over at perl v5.32.1. it's giving interface, it's giving "collection of things", and we're gonna walk through it together. no cap. ✨

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🌸 NAME 🌸

Bio::SeqFeature::CollectionI — it's literally an interface for a collection of Bio::SeqFeatureI objects. that's the whole vibe. 💅

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🦋 SYNOPSIS 🦋

so like, you get a Bio::SeqFeature::CollectionI somehow — maybe a Bio::SeqFeature::Collection, iykyk — and then:

# get a Bio::SeqFeature::CollectionI somehow # perhaps a
# Bio::SeqFeature::Collection

    use Bio::SeqFeature::Collection;
    my $collection = Bio::SeqFeature::Collection->new();
    $collection->add_features(\@featurelist);

    $collection->features(-attributes =>
                          [ { 'location' => Bio::Location::Simple->new
                                  (-start=> 1, -end => 300) ,
                                  'overlaps' }]);

look at her go. iconic. 👑

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🎀 DESCRIPTION 🎀

this interface describes the basic methods you need for a collection of Sequence Features. that's it, that's the whole job, and she does it beautifully. periodt. 💖

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🌈 FEEDBACK 🌈

💌 Mailing Lists 💌

user feedback is an integral part of the evolution of this and other Bioperl modules — fr fr, they actually want to hear from you. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated, bestie. 🫶

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. like, no shade to the maintainer, it's just that many experienced and responsive 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 deets the better, bestie. 🙈

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

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

not me asking you to file an issue, but like, please do. 💀

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👑 AUTHOR - Jason Stajich 👑

email jason@bioperl.org — shoutout to Jason for real. 🫡

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✨ APPENDIX ✨

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that's your cue, iykyk. 🔍

🍓 add_features 🍓

• Title: add_features
• Usage: $collection->add_features(\@features);
• Function: (not specified — she's mysterious like that)
• Returns: number of features added
• Args: arrayref of Bio::SeqFeatureI objects to index

so you hand her an arrayref of Bio::SeqFeatureI objects and she indexes them, then tells you how many she added. simple. slay. 💅

🧚 features 🧚

• Title: features
• Usage: my @f = $collection->features(@args);
• Returns: a list of Bio::SeqFeatureI objects
• Args: see below
• Status: public

this routine will retrieve features associated with this collection object. it can be used to return all features, or a subset based on their type, location, or attributes. so many options, we love a flexible queen. 👑

• -types — list of feature types to return. the argument is an array of Bio::Das::FeatureTypeI objects or a set of strings that can be converted into FeatureTypeI objects.
• -callback — a callback to invoke on each feature. the subroutine will be passed to each Bio::SeqFeatureI object in turn.
• -attributes — a hash reference containing attributes to match.

the -attributes argument is a hashref containing one or more attributes to match against:

-attributes => { Gene => 'abc-1',
                 Note => 'confirmed' }

attribute matching is simple exact string matching, and multiple attributes are ANDed together. see Bio::DB::ConstraintsI for a more sophisticated take on this. ✨

if one provides a callback, it will be invoked on each feature in turn. if the callback returns a false value, iteration will be interrupted. when a callback is provided, the method returns undef. 👀

heads up bestie: callback returns false → iteration gets interrupted, and the method hands you back undef. plan accordingly. 💖

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and that's the whole page, gorgeous. this was the Bio::S...ctionI(3pm) manpage from the User Contributed Perl Documentation, shipped with perl v5.32.1, dated 2021-08-15. mwah. go build something iconic with your feature collection. 🎀💜🦋✨