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

💖 Bio::Graphics::Feature 💖

okay so before we even start: this page is Bio::Graphics::Feature, from the User Contributed Perl Documentation, manual section 3pm. yes bestie we're reading perl docs for fun now, it's giving glow-up era 🦋

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✨ NAME ✨

Bio::Graphics::Feature — a simple feature object for use with Bio::Graphics::Panel. that's it, that's the whole job, and she does it beautifully 💅

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🌸 SYNOPSIS 🌸

use Bio::Graphics::Feature;

# create a simple feature with no internal structure
$f = Bio::Graphics::Feature->new(-start => 1000,
                                 -stop  => 2000,
                                 -type  => 'transcript',
                                 -name  => 'alpha-1 antitrypsin',
                                 -desc  => 'an enzyme inhibitor',
                                );

# create a feature composed of multiple segments, all of type "similarity"
$f = Bio::Graphics::Feature->new(-segments => [[1000,1100],[1500,1550],[1800,2000]],
                                 -name     => 'ABC-3',
                                 -type     => 'gapped_alignment',
                                 -subtype  => 'similarity');

# build up a gene exon by exon
$e1 = Bio::Graphics::Feature->new(-start=>1,-stop=>100,-type=>'exon');
$e2 = Bio::Graphics::Feature->new(-start=>150,-stop=>200,-type=>'exon');
$e3 = Bio::Graphics::Feature->new(-start=>300,-stop=>500,-type=>'exon');
$f  = Bio::Graphics::Feature->new(-segments=>[$e1,$e2,$e3],-type=>'gene');

like??? three whole ways to build a feature, no cap, pick your fighter 💀

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🎀 DESCRIPTION 🎀

This is a simple Bio::SeqFeatureI-compliant object that's compatible with Bio::Graphics::Panel. Translation: it's your lowkey lightweight feature object, and you use it to draw stuff. lightweight is the key word here — she's not carrying any baggage, she just shows up and renders. 👑

All the methods work exactly like Bio::SeqFeatureI describes, PLUS the following additions, which we're about to go through one by one because I love you and I want you to actually understand it 🫶

🧚 The new() Constructor

$feature = Bio::Graphics::Feature->new(@args);

This method creates a brand new feature object. You can make a simple feature with no subfeatures at all, or you can go full main-character and build a hierarchically nested object. either way, slay.

Arguments are as follows:

• -seq_id — the reference sequence
• -start — the start position of the feature
• -end — the stop position of the feature
• -stop — an alias for -end
• -name — the feature name (returned by seqname())
• -type — the feature type (returned by primary_tag())
• -primary_tag — the same as -type
• -source — the source tag
• -score — the feature score (for GFF compatibility)
• -desc — a description of the feature
• -segments — a list of subfeatures (see below)
• -subtype — the type to use when creating subfeatures
• -strand — the strand of the feature (one of -1, 0 or +1)
• -phase — the phase of the feature (0..2)
• -id — an alias for -name
• -seqname — an alias for -name
• -display_id — an alias for -name
• -display_name — an alias for -name (do you get the idea the API has changed?)
• -primary_id — unique database ID
• -url — a URL to link to when rendered with Bio::Graphics
• -configurator — an object (like a Bio::Graphics::FeatureFile) that knows how to configure the graphical representation of the object based on its type.
• -attributes — a hashref of tag value attributes, in which the key is the tag and the value is an array reference of values
• -factory — a reference to a feature factory, used for compatibility with more obscure parts of Bio::DB::GFF

The subfeatures you pass in -segments can be an array of Bio::Graphics::Feature objects, or an array of [$start,$stop] pairs. each pair should be a two-element array reference, bestie, don't get cute with it. in the latter case, the feature type you passed in -subtype gets used when creating the subfeatures. ✨

If no feature type is passed, then it defaults to "feature". no drama, it just picks one for you.

🦋 Non-SeqFeatureI methods

A bunch of new methods are provided for compatibility with Ace::Sequence, which has a slightly different API from SeqFeatureI. it's giving "we've known each other for years but we speak different dialects" 😭

attributes() : An alternative interface to get_tag_values. Pass the name of an attribute and you get the value(s) of that attribute:

$expression_level = $gene->attributes('expression');

Call attributes() with no arguments at all and you get a hash of every attribute:

%attributes = $gene->attributes;

url() : Get/set the URL that the graphical rendering of this feature will link to.

add_segment(@segments) : Add one or more segments (a subfeature). Segments can either be Feature objects, or [start,stop] arrays, exactly like the -segments argument to new(). The feature endpoints are automatically adjusted. she fixes the math for you, iconic behavior.

my @features = get_SeqFeatures('type1','type2','type3'...) : Get the subfeatures of this feature. If you hand it an optional list of types, then it only returns subfeatures with the indicated primary_tag. (This is an extension of the Bio::SeqFeatureI interface — we're doing extra credit here.)

$feature->add_hit($hit) : For nucleotide alignments, add a feature that is a "hit" on the feature.

$hit = $feature->hit : Return the hit.

segments() : An alias for get_SeqFeatures().

get_all_SeqFeatures() : Alias for get_SeqFeatures()

merged_segments() : Another alias for sub_SeqFeature().

stop() : An alias for end().

name() : An alias for seqname().

exons() : An alias for sub_SeqFeature() (you don't want to know why!)

configurator() : Get/set the configurator that knows how to adjust the graphical representation of this feature based on its type. Currently the only configurator that will work is Bio::Graphics::FeatureFile.

so many aliases bestie. they're all the same method wearing different outfits. it's called ✨fashion✨

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💜 factory

• Title: factory
• Usage: $factory = $obj->factory([$new_factory])
• Function: Returns the feature factory from which this feature was generated. Mostly for compatibility with weird dependencies in gbrowse.
• Returns: A feature factory
• Args: None

💜 display_name

• Title: display_name
• Usage: $id = $obj->display_name or $obj->display_name($newid);
• Function: Gets or sets the display id, also known as the common name of the Seq object.

The semantics of this is that it is the most likely string to be used as an identifier of the sequence, and likely to have "human" readability. The id is equivalent to the LOCUS field of the GenBank/EMBL databanks and the ID field of the Swissprot/sptrembl database. In fasta format, the >(\S+) is presumed to be the id, though some people overload the id to embed other information. Bioperl does not use any embedded information in the ID field, and people are encouraged to use other mechanisms (accession field for example, or extending the sequence object) to solve this.

Notice that $seq->id() maps to this function, mainly for legacy/convenience issues.

• Returns: A string
• Args: None or a new id

💜 accession_number

• Title: accession_number
• Usage: $unique_biological_key = $obj->accession_number;
• Function: Returns the unique biological id for a sequence, commonly called the accession_number. For sequences from established databases, the implementors should try to use the correct accession number. Notice that primary_id() provides the unique id for the implementation, allowing multiple objects to have the same accession number in a particular implementation.

For sequences with no accession number, this method should return "unknown".

• Returns: A string
• Args: None

💜 alphabet

• Title: alphabet
• Usage: if( $obj->alphabet eq 'dna' ) { /Do Something/ }
• Function: Returns the type of sequence being one of 'dna', 'rna' or 'protein'. This is case sensitive.

This is not called <type> because this would cause upgrade problems from the 0.5 and earlier Seq objects.

• Returns: a string either 'dna','rna','protein'. NB - the object must make a call of the type - if there is no type specified it has to guess.
• Args: none
• Status: Virtual

she has to GUESS?? yes bestie. no type, no info, she's just out here vibing and inferring. 😭

💜 desc

• Title: desc
• Usage: $seqobj->desc($string) or $seqobj->desc()
• Function: Sets or gets the description of the sequence
• Example:
• Returns: The description
• Args: The description or none

💜 location

• Title: location
• Usage: my $location = $seqfeature->location()
• Function: returns a location object suitable for identifying location of feature on sequence or parent feature
• Returns: Bio::LocationI object
• Args: none

💜 location_string

• Title: location_string
• Usage: my $string = $seqfeature->location_string()
• Function: Returns a location string in a format recognized by gbrowse
• Returns: a string
• Args: none

This is a convenience function used by the generic genome browser. It returns the location of the feature and its subfeatures in the compact form "start1..end1,start2..end2,...". Use $seqfeature->location()->toFTString() to obtain a standard GenBank/EMBL location representation. compact queen.

💜 configurator

• Title: configurator
• Usage: my $configurator = $seqfeature->configurator([$new_configurator])
• Function: Get/set an object that provides configuration information for this feature
• Returns: configurator object
• Args: new configurator object (optional)

A configurator object provides hints to the Bio::Graphics::Feature as to how to display itself on a canvas. Currently this stores the Bio::Graphics::FeatureFile and descendents.

💜 url

• Title: url
• Usage: my $url = $seqfeature->url([$new_url])
• Function: Get/set the URL associated with this feature
• Returns: a URL string
• Args: new URL (optional)

Features link to URLs when displayed as a clickable image map. This field holds that information.

💜 make_link

• Title: make_link
• Usage: my $url = $seqfeature->make_link()
• Function: Create a URL for the feature
• Returns: a URL string
• Args: none

This method will invoke the configurator in order to turn the feature into a link. Used by Bio::Graphics::Panel to create imagemaps. 🔗

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🌈 SEE ALSO 🌈

Bio::Graphics::Panel,Bio::Graphics::Glyph, Bio::Graphics::FeatureBase GD

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👑 AUTHOR 👑

Lincoln Stein <lstein@cshl.edu>.

Copyright (c) 2001 Cold Spring Harbor Laboratory

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.

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and that's the whole page bestie, you made it, I'm so proud of you 🥹🫶 go forth and draw your features, you absolute icon 💅✨

perl v5.30.0 · 2019-11-25 · Bio::G...eature(3pm) — mwah, thanks for reading, no cap 💖