SYNOPSIS
See Bio::DB::GFF.DESCRIPTION
Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too, if needed).Bio::DB::GFF::Feature adds new methods to retrieve the annotation type, group, and other GFF attributes. Annotation types are represented by Bio::DB::GFF::Typename objects, a simple class that has two methods called method() and source(). These correspond to the method and source fields of a GFF file.
Annotation groups serve the dual purpose of giving the annotation a human-readable name, and providing higher-order groupings of subfeatures into features. The groups returned by this module are objects of the Bio::DB::GFF::Featname class.
Bio::DB::GFF::Feature inherits from and implements the abstract methods of Bio::SeqFeatureI, allowing it to interoperate with other Bioperl modules.
Generally, you will not create or manipulate Bio::DB::GFF::Feature objects directly, but use those that are returned by the Bio::DB::GFF::RelSegment->features() method.
Important note about start() vs end()
If features are derived from segments that use relative addressing (which is the default), then start() will be less than end() if the feature is on the opposite strand from the reference sequence. This breaks Bio::SeqI compliance, but is necessary to avoid having the real genomic locations designated by start() and end() swap places when changing reference points.To avoid this behavior, call $segment->absolute(1) before fetching features from it. This will force everything into absolute coordinates.
For example:
my $segment = $db->segment('CHROMOSOME_I');
$segment->absolute(1);
my @features = $segment->features('transcript');
API
The remainder of this document describes the public and private methods implemented by this module.new_from_parent
Title : new_from_parent Usage : $f = Bio::DB::GFF::Feature->new_from_parent(@args); Function: create a new feature object Returns : new Bio::DB::GFF::Feature object Args : see below Status : Internal
This method is called by Bio::DB::GFF to create a new feature using information obtained from the GFF database. It is one of two similar constructors. This one is called when the feature is generated from a RelSegment object, and should inherit the coordinate system of that object.
The 13 arguments are positional (sorry):
$parent a Bio::DB::GFF::RelSegment object (or descendent)
$start start of this feature
$stop stop of this feature
$method this feature's GFF method
$source this feature's GFF source
$score this feature's score
$fstrand this feature's strand (relative to the source
sequence, which has its own strandedness!)
$phase this feature's phase
$group this feature's group (a Bio::DB::GFF::Featname object)
$db_id this feature's internal database ID
$group_id this feature's internal group database ID
$tstart this feature's target start
$tstop this feature's target stop
tstart and tstop are not used for anything at the moment, since the information is embedded in the group object.
new
Title : new Usage : $f = Bio::DB::GFF::Feature->new(@args); Function: create a new feature object Returns : new Bio::DB::GFF::Feature object Args : see below Status : Internal
This method is called by Bio::DB::GFF to create a new feature using information obtained from the GFF database. It is one of two similar constructors. This one is called when the feature is generated without reference to a RelSegment object, and should therefore use its default coordinate system (relative to itself).
The 11 arguments are positional:
$factory a Bio::DB::GFF adaptor object (or descendent)
$srcseq the source sequence
$start start of this feature
$stop stop of this feature
$method this feature's GFF method
$source this feature's GFF source
$score this feature's score
$fstrand this feature's strand (relative to the source
sequence, which has its own strandedness!)
$phase this feature's phase
$group this feature's group
$db_id this feature's internal database ID
type
Title : type Usage : $type = $f->type([$newtype]) Function: get or set the feature type Returns : a Bio::DB::GFF::Typename object Args : a new Typename object (optional) Status : Public
This method gets or sets the type of the feature. The type is a Bio::DB::GFF::Typename object, which encapsulates the feature method and source.
The method() and source() methods described next provide shortcuts to the individual fields of the type.
method
Title : method Usage : $method = $f->method([$newmethod]) Function: get or set the feature method Returns : a string Args : a new method (optional) Status : Public
This method gets or sets the feature method. It is a convenience feature that delegates the task to the feature's type object.
source
Title : source Usage : $source = $f->source([$newsource]) Function: get or set the feature source Returns : a string Args : a new source (optional) Status : Public
This method gets or sets the feature source. It is a convenience feature that delegates the task to the feature's type object.
score
Title : score Usage : $score = $f->score([$newscore]) Function: get or set the feature score Returns : a string Args : a new score (optional) Status : Public
This method gets or sets the feature score.
phase
Title : phase Usage : $phase = $f->phase([$phase]) Function: get or set the feature phase Returns : a string Args : a new phase (optional) Status : Public
This method gets or sets the feature phase.
strand
Title : strand Usage : $strand = $f->strand Function: get the feature strand Returns : +1, 0 -1 Args : none Status : Public
Returns the strand of the feature. Unlike the other methods, the strand cannot be changed once the object is created (due to coordinate considerations).
group
Title : group Usage : $group = $f->group([$new_group]) Function: get or set the feature group Returns : a Bio::DB::GFF::Featname object Args : a new group (optional) Status : Public
This method gets or sets the feature group. The group is a Bio::DB::GFF::Featname object, which has an ID and a class.
display_id
Title : display_id Usage : $display_id = $f->display_id([$display_id]) Function: get or set the feature display id Returns : a Bio::DB::GFF::Featname object Args : a new display_id (optional) Status : Public
This method is an alias for group(). It is provided for Bio::SeqFeatureI compatibility.
info
Title : info Usage : $info = $f->info([$new_info]) Function: get or set the feature group Returns : a Bio::DB::GFF::Featname object Args : a new group (optional) Status : Public
This method is an alias for group(). It is provided for AcePerl compatibility.
target
Title : target Usage : $target = $f->target([$new_target]) Function: get or set the feature target Returns : a Bio::DB::GFF::Homol object Args : a new group (optional) Status : Public
This method works like group(), but only returns the group if it implements the start() method. This is typical for similarity/assembly features, where the target encodes the start and stop location of the alignment.
The returned object is of type Bio::DB::GFF::Homol, which is a subclass of Bio::DB::GFF::Segment.
flatten_target
Title : flatten_target Usage : $target = $f->flatten_target($f->target) Function: flatten a target object Returns : a string (GFF2), an array [GFF2.5] or an array ref [GFF3] Args : a target object (required), GFF version (optional) Status : Public
This method flattens a target object into text for GFF dumping. If a second argument is provided, version-specific vocabulary is used for the flattened target.
hit
Title : hit Usage : $hit = $f->hit([$new_hit]) Function: get or set the feature hit Returns : a Bio::DB::GFF::Featname object Args : a new group (optional) Status : Public
This is the same as target(), for compatibility with Bio::SeqFeature::SimilarityPair.
id
Title : id Usage : $id = $f->id Function: get the feature ID Returns : a database identifier Args : none Status : Public
This method retrieves the database identifier for the feature. It cannot be changed.
group_id
Title : group_id Usage : $id = $f->group_id Function: get the feature ID Returns : a database identifier Args : none Status : Public
This method retrieves the database group identifier for the feature. It cannot be changed. Often the group identifier is more useful than the feature identifier, since it is used to refer to a complex object containing subparts.
clone
Title : clone Usage : $feature = $f->clone Function: make a copy of the feature Returns : a new Bio::DB::GFF::Feature object Args : none Status : Public
This method returns a copy of the feature.
compound
Title : compound Usage : $flag = $f->compound([$newflag]) Function: get or set the compound flag Returns : a boolean Args : a new flag (optional) Status : Public
This method gets or sets a flag indicated that the feature is not a primary one from the database, but the result of aggregation.
sub_SeqFeature
Title : sub_SeqFeature Usage : @feat = $feature->sub_SeqFeature([$method]) Function: get subfeatures Returns : a list of Bio::DB::GFF::Feature objects Args : a feature method (optional) Status : Public
This method returns a list of any subfeatures that belong to the main feature. For those features that contain heterogeneous subfeatures, you can retrieve a subset of the subfeatures by providing a method name to filter on.
This method may also be called as segments() or get_SeqFeatures().
add_subfeature
Title : add_subfeature Usage : $feature->add_subfeature($feature) Function: add a subfeature to the feature Returns : nothing Args : a Bio::DB::GFF::Feature object Status : Public
This method adds a new subfeature to the object. It is used internally by aggregators, but is available for public use as well.
attach_seq
Title : attach_seq
Usage : $sf->attach_seq($seq)
Function: Attaches a Bio::Seq object to this feature. This
Bio::Seq object is for the *entire* sequence: ie
from 1 to 10000
Example :
Returns : TRUE on success
Args : a Bio::PrimarySeqI compliant object
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
entire_seq
Title : entire_seq
Usage : $whole_seq = $sf->entire_seq()
Function: gives the entire sequence that this seqfeature is attached to
Example :
Returns : a Bio::PrimarySeqI compliant object, or undef if there is no
sequence attached
Args : none
merged_segments
Title : merged_segments Usage : @segs = $feature->merged_segments([$method]) Function: get merged subfeatures Returns : a list of Bio::DB::GFF::Feature objects Args : a feature method (optional) Status : Public
This method acts like sub_SeqFeature, except that it merges overlapping segments of the same time into contiguous features. For those features that contain heterogeneous subfeatures, you can retrieve a subset of the subfeatures by providing a method name to filter on.
A side-effect of this method is that the features are returned in sorted order by their start tposition.
sub_types
Title : sub_types Usage : @methods = $feature->sub_types Function: get methods of all sub-seqfeatures Returns : a list of method names Args : none Status : Public
For those features that contain subfeatures, this method will return a unique list of method names of those subfeatures, suitable for use with sub_SeqFeature().
attributes
Title : attributes Usage : @attributes = $feature->attributes($name) Function: get the "attributes" on a particular feature Returns : an array of string Args : feature ID Status : public
Some GFF version 2 files use the groups column to store a series of attribute/value pairs. In this interpretation of GFF, the first such pair is treated as the primary group for the feature; subsequent pairs are treated as attributes. Two attributes have special meaning: ``Note'' is for backward compatibility and is used for unstructured text remarks. ``Alias'' is considered as a synonym for the feature name.
@gene_names = $feature->attributes('Gene');
@aliases = $feature->attributes('Alias');
If no name is provided, then attributes() returns a flattened hash, of attribute=>value pairs. This lets you do:
%attributes = $db->attributes;
notes
Title : notes Usage : @notes = $feature->notes Function: get the "notes" on a particular feature Returns : an array of string Args : feature ID Status : public
Some GFF version 2 files use the groups column to store various notes and remarks. Adaptors can elect to store the notes in the database, or just ignore them. For those adaptors that store the notes, the notes() method will return them as a list.
aliases
Title : aliases Usage : @aliases = $feature->aliases Function: get the "aliases" on a particular feature Returns : an array of string Args : feature ID Status : public
This method will return a list of attributes of type 'Alias'.
Autogenerated Methods
Title : AUTOLOAD Usage : @subfeat = $feature->Method Function: Return subfeatures using autogenerated methods Returns : a list of Bio::DB::GFF::Feature objects Args : none Status : Public
Any method that begins with an initial capital letter will be passed to AUTOLOAD and treated as a call to sub_SeqFeature with the method name used as the method argument. For instance, this call:
@exons = $feature->Exon;
is equivalent to this call:
@exons = $feature->sub_SeqFeature('exon');
SeqFeatureI methods
The following Bio::SeqFeatureI methods are implemented:primary_tag(), source_tag(), all_tags(), has_tag(), each_tag_value() [renamed get_tag_values()].
adjust_bounds
Title : adjust_bounds Usage : $feature->adjust_bounds Function: adjust the bounds of a feature Returns : ($start,$stop,$strand) Args : none Status : Public
This method adjusts the boundaries of the feature to enclose all its subfeatures. It returns the new start, stop and strand of the enclosing feature.
sort_features
Title : sort_features Usage : $feature->sort_features Function: sort features Returns : nothing Args : none Status : Public
This method sorts subfeatures in ascending order by their start position. For reverse strand features, it sorts subfeatures in descending order. After this is called sub_SeqFeature will return the features in order.
This method is called internally by merged_segments().
asString
Title : asString Usage : $string = $feature->asString Function: return human-readabled representation of feature Returns : a string Args : none Status : Public
This method returns a human-readable representation of the feature and is called by the overloaded "" operator.
gff_string
Title : gff_string Usage : $string = $feature->gff_string Function: return GFF2 of GFF2.5 representation of feature Returns : a string Args : none Status : Public
gff3_string
Title : gff3_string
Usage : $string = $feature->gff3_string([$recurse])
Function: return GFF3 representation of feature
Returns : a string
Args : An optional flag, which if true, will cause the feature to recurse over
subfeatures.
Status : Public
version
Title : version Usage : $feature->version() Function: get/set the GFF version to be returned by gff_string Returns : the GFF version (default is 2) Args : the GFF version (2, 2.5 of 3) Status : Public
cmap_link()
Title : cmap_link Usage : $link = $feature->cmap_link Function: returns a URL link to the corresponding feature in cmap Returns : a string Args : none Status : Public
If integrated cmap/gbrowse installation, it returns a link to the map otherwise it returns a link to a feature search on the feature name. See the cmap documentation for more information.
This function is intended primarily to be used in gbrowse conf files. For example:
link = sub {my $self = shift; return $self->cmap_viewer_link(data_source);}
A Note About Similarities
The current default aggregator for GFF ``similarity'' features creates a composite Bio::DB::GFF::Feature object of type ``gapped_alignment''. The target() method for the feature as a whole will return a RelSegment object that is as long as the extremes of the similarity hit target, but will not necessarily be the same length as the query sequence. The length of each ``similarity'' subfeature will be exactly the same length as its target(). These subfeatures are essentially the HSPs of the match.The following illustrates this:
@similarities = $segment->feature('similarity:BLASTN');
$sim = $similarities[0];
print $sim->type; # yields "gapped_similarity:BLASTN"
$query_length = $sim->length;
$target_length = $sim->target->length; # $query_length != $target_length
@matches = $sim->Similarity; # use autogenerated method
$query1_length = $matches[0]->length;
$target1_length = $matches[0]->target->length; # $query1_length == $target1_length
If you merge segments by calling merged_segments(), then the length of the query sequence segments will no longer necessarily equal the length of the targets, because the alignment information will have been lost. Nevertheless, the targets are adjusted so that the first and last base pairs of the query match the first and last base pairs of the target.
BUGS
This module is still under development.AUTHOR
Lincoln Stein <[email protected]>.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.