NAME

Bio::DB::GFF::Feature -- A relative segment identified by a feature type

SYNOPSIS

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's 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 that object's coordinate system.

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 aren't 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::Featname 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.

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.

For AcePerl compatibility, this method may also be called as segments().

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.

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 <lstein@cshl.org>.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

To install LocalConfig, copy and paste the appropriate command in to your terminal.

cpanm

cpanm LocalConfig

CPAN shell

perl -MCPAN -e shell
install LocalConfig

For more information on module installation, please visit the detailed CPAN module installation guide.

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