Bio::G...nSearch(3pm)

💖 Bio::Graphics::Browser2::RegionSearch — bestie edition 💖

okay so this is Bio::Graphics::Browser2::RegionSearch, straight outta the User Contributed Perl Documentation. It's a Perl module, it lives in Bio::G...nSearch(3pm), and it's literally here to search through multiple databases for feature matches. slay. 🦋

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✨ NAME ✨

Bio::Graphics::Browser2::RegionSearch — Search through multiple databases for feature matches. 💅

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🌸 SYNOPSIS 🌸

my $dbs = Bio::Graphics::Browser2::RegionSearch->new(
            { source => $data_source,
              state  => $session_state
            });
$dbs->init_databases();
my $features = $dbs->search_features({-search_term=>'sma-3'});

that's the whole vibe right there. make the object, init the dbs, search the features. no cap. ✨

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🎀 DESCRIPTION 🎀

so this implements a feature search based on the heuristics in Bio::Graphics::Browser2::Region. and the search? it's distributed across all local and remote databases as specified in the data source. she's everywhere. main character energy fr fr. 👑

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💜 METHODS 💜

the remainder of this document describes the methods available to the programmer. iykyk. 💅

🫶 $db = Bio::Graphics::Browser2::RegionSearch->new({opts})

Create a new RegionSearch object. the required parameters are:

• source — the Bio::Graphics::Browser2::DataSource object describing the local and remote databases for this source.
• state — the page_settings document describing the current state of the user session (for looking up search_options and the like in the future).

🧚 $db->init_databases(\@labels)

This method will initialize all the databases in preparation for a search. Pass it a list of track labels to search only in the databases defined by those tracks. Otherwise it will sort all tracks into local and remote ones. lowkey the multitasker of the module. 💖

⭐ $source = source()

Return the data source.

🌈 state()

🌈 remote_dbs()

🌈 local_dbs()

(yes bestie, those three are just listed like that, they're methods, go off 👑)

💫 @features = $db->features(@args)

Pass @args to the underlying db adaptors' features() methods and return all matching features. Example:

@features = $db->features(-type=>'CDS')

🦋 $meta_segment = $db->segment($segment)

Given an existing segment, return a Bio::Graphics::Browser2::MetaSegment object, which behaves more or less like a regular Bio::Das::SegmentI object, but searches multiple databases. Both iterative and non-iterative feature fetching is supported.

(the class definitions for Bio::Graphics::Browser2::MetaSegment are located in the Bio/Graphics/Browser/RegionSearch.pm file.) 💅

🌸 $segment = $db->feature2segment($feature)

Converts a feature into a segment in the database that the feature corresponds to.

🎀 @segments = $db->features2segments($feature)

As above, but takes an arrayref of features and returns an array of segments.

🔥 $found = $db->search_features($args)

This method will search all the databases for features matching the search term and will return the results as an array ref of Bio::SeqFeatureI objects. The arguments are a hash ref containing the various options passed to the db adaptors' features() method (e.g. "-type"), or a hashref with the key "-search_term", in which case the search term is parsed as any of gbrowse's heuristic keyword searches.

If no args are provided, then the search term is taken from the "name" field of the settings object.

💖 $found = $db->search_features_locally($args)

Search only the local databases for the term.

$Args is a hashref:

• -search_term — term to search for
• -shortcircuit — stop searching if term is found in default db

If -shortcircuit is not provided, it defaults to true.

🌈 $found = $db->search_features_remotely($args)

Search only the remote databases for the term.

👑 $db->add_dbid_to_features($db,$features)

Add a gbrowse_dbid() method to each of the features in the list.

✨ $mapper = $search->coordinate_mapper($segment,$optimize)

Create a Bio::Graphics coordinator mapper on the current segment. If optimize set to true, then features that map outside the current segment's seqid and region are nulled.

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🌟 SEE ALSO 🌟

• Bio::Graphics::Browser2::Region
• Bio::Graphics::Browser
• Bio::Graphics::Feature

go read those too bestie, they're the friend group 💜

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🫶 AUTHOR 🫶

Lincoln Stein <lincoln.stein@gmail.com>.

Copyright (c) 2008 Cold Spring Harbor Laboratory & Ontario Institute for Cancer Research

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.

fr fr, read LICENSE and DISCLAIMER.txt before you go doing anything wild with this. legal girlies stay winning 💅

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and that's the whole page, bestie!! this one came from perl v5.40.0, dated 2024-10-20, and it's the Bio::G...nSearch(3pm) manpage. mwah. 💖✨🎀🦋🌸