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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute
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<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::Feature - Ensembl specific sequence feature.
SYNOPSIS
my $feat = new Bio::EnsEMBL::Feature(
-start => 100,
-end => 220,
-strand => -1,
-slice => $slice,
-analysis => $analysis
);
my $start = $feat->start();
my $end = $feat->end();
my $strand = $feat->strand();
# Move the feature to the chromosomal coordinate system
$feature = $feature->transform('chromosome');
# Move the feature to a different slice (possibly on another coord
# system)
$feature = $feature->transfer($new_slice);
# Project the feature onto another coordinate system possibly across
# boundaries:
@projection = @{ $feature->project('contig') };
# Change the start, end, and strand of the feature in place
$feature->move( $new_start, $new_end, $new_strand );DESCRIPTION
This is the Base feature class from which all Ensembl features inherit. It provides a bare minimum functionality that all features require. It basically describes a location on a sequence in an arbitrary coordinate system.
METHODS
new
Arg [-SLICE]: Bio::EnsEMBL::SLice - Represents the sequence that this
feature is on. The coordinates of the created feature are
relative to the start of the slice.
Arg [-START]: The start coordinate of this feature relative to the start
of the slice it is sitting on. Coordinates start at 1 and
are inclusive.
Arg [-END] : The end coordinate of this feature relative to the start of
the slice it is sitting on. Coordinates start at 1 and are
inclusive.
Arg [-STRAND]: The orientation of this feature. Valid values are 1,-1,0.
Arg [-SEQNAME] : A seqname to be used instead of the default name of the
of the slice. Useful for features that do not have an
attached slice such as protein features.
Arg [-dbID] : (optional) internal database id
Arg [-ADAPTOR]: (optional) Bio::EnsEMBL::DBSQL::BaseAdaptor
Example : $feature = Bio::EnsEMBL::Feature->new(-start => 1,
-end => 100,
-strand => 1,
-slice => $slice,
-analysis => $analysis);
Description: Constructs a new Bio::EnsEMBL::Feature. Generally subclasses
of this method are instantiated, rather than this class itself.
Returntype : Bio::EnsEMBL::Feature
Exceptions : Thrown on invalid -SLICE, -ANALYSIS, -STRAND ,-ADAPTOR arguments
Caller : general, subclass constructors
Status : Stablestart
Arg [1] : (optional) int $start
The start of this feature relative to the start of the slice
that it is on.
Example : $start = $feat->start()
Description: Getter/Setter for the start of this feature relative to the
start of the slice it is on. Note that negative values, or
values exceeding the length of the slice are permitted.
Start must be less than or equal to the end regardless of the
strand. Coordinate values start at 1 and are inclusive.
Returntype : int
Exceptions : none
Caller : general
Status : Stableend
Arg [1] : (optional) int $end
Example : $end = $feat->end();
Description: Getter/Setter for the end of this feature relative to the
start of the slice that it is on. Note that negative values,
of values exceeding the length of the slice are permitted. End
must be greater than or equal to start regardless of the strand.
Coordinate values start at 1 and are inclusive.
Returntype : int
Exceptions : none
Caller : general
Status : Stablestrand
Arg [1] : (optional) int $strand
Example : $feat->strand(-1);
Description: Getter/Setter for the strand of this feature relative to the
slice it is on. 0 is an unknown or non-applicable strand.
-1 is the reverse (negative) strand and 1 is the forward
(positive) strand. No other values are permitted.
Returntype : int
Exceptions : thrown if an invalid strand argument is passed
Caller : general
Status : Stablemove
Arg [1] : int start
Arg [2] : int end
Arg [3] : (optional) int strand
Description: Sets the start, end and strand in one call rather than in
3 seperate calls to the start(), end() and strand() methods.
This is for convenience and for speed when this needs to be
done within a tight loop.
Returntype : none
Exceptions : Thrown is invalid arguments are provided
Caller : general
Status : Stablelength
Arg [1] : none
Example : $length = $feat->length();
Description: Returns the length of this feature
Returntype : Integer
Exceptions : Throws if end < start and the feature is not on a
circular slice
Caller : general
Status : Stableanalysis
Arg [1] : (optional) Bio::EnsEMBL::Analysis $analysis
Example : $feature->analysis(new Bio::EnsEMBL::Analysis(...))
Description: Getter/Setter for the analysis that is associated with
this feature. The analysis describes how this feature
was derived.
Returntype : Bio::EnsEMBL::Analysis
Exceptions : thrown if an invalid argument is passed
Caller : general
Status : Stableslice
Arg [1] : (optional) Bio::EnsEMBL::Slice $slice
Example : $seqname = $feature->slice()->name();
Description: Getter/Setter for the Slice that is associated with this
feature. The slice represents the underlying sequence that this
feature is on. Note that this method call is analagous to the
old SeqFeature methods contig(), entire_seq(), attach_seq(),
etc.
Returntype : Bio::EnsEMBL::Slice
Exceptions : thrown if an invalid argument is passed
Caller : general
Status : Stableequals
Arg [1] : Bio::EnsEMBL::Feature object
Example : if ($featureA->equals($featureB)) { ... }
Description : Compares two features using various criteria. The
test for eqality goes through the following list and
terminates at the first true match:
1. If the two features are the same object, they are
equal.
2. If they are of different types (e.g., transcript
and gene), they are *not* equal.
3. If they both have dbIDs: if these are the same,
then they are equal, otherwise not.
4. If they both have slices and analysis objects:
if the analysis dbIDs are the same and the
seq_region_id are the same, along with
seq_region_start and seq_region_end, then they are
equal, otherwise not.
If none of the above is able to determine equality,
undef is returned.
Return type : tri-Boolean (0, 1, undef = "unknown")
Exceptions : Thrown if a non-feature is passed as the argument.transform
Arg [1] : string $coord_system
The coord system to transform this feature to.
Arg [2] : string $version (optional)
The version of the coord system to transform this feature to.
Arg [3] : Bio::EnsEMBL::Slice (optional)
Specified when a projection may land on many overlapping slices
and disambiguation is required.
Example : $feature = $feature->transform('contig');
next if(!defined($feature));
Description: Returns a copy of this feature, but converted to a different
coordinate system. The converted feature will be placed on a
slice which spans an entire sequence region of the new
coordinate system. If the requested coordinate system is the
same coordinate system it is simply placed on a slice which
spans the entire seq_region (as opposed to the original slice
which may have only partially covered the seq_region).
If a feature spans a boundary in the new coordinate system,
undef is returned instead.
For example, transforming an exon in contig coordinates to one
in chromosomal coodinates will place the exon on a slice of an
entire chromosome.
Returntype : Bio::EnsEMBL::Feature (or undef)
Exceptions : thrown if an invalid coordinate system is provided
warning if Feature is not attached to a slice
Caller : general, transfer()
Status : Stabletransfer
Arg [1] : Bio::EnsEMBL::Slice $slice
The slice to transfer this feature to
Example : $feature = $feature->transfer($slice);
next if(!defined($feature));
Description: Returns a copy of this feature which has been shifted onto
another slice.
If the new slice is in a different coordinate system the
feature is transformed first and then placed on the slice.
If the feature would be split across a coordinate system
boundary or mapped to a gap undef is returned instead.
If the feature cannot be placed on the provided slice because
it maps to an entirely different location, undef is returned
instead.
Returntype : Bio::EnsEMBL::Feature (or undef)
Exceptions : throw on incorrect argument
throw if feature does not have attached slice
Caller : general, transform()
Status : Stableproject_to_slice
Arg [1] : slice to project to
Example :
my $clone_projection = $feature->project_to_slice($slice);
foreach my $seg (@$clone_projection) {
my $clone = $seg->to_Slice();
print "Features current coords ", $seg->from_start, '-',
$seg->from_end, " project onto clone coords " .
$clone->seq_region_name, ':', $clone->start, '-', $clone->end,
$clone->strand, "\n";
}
Description: Returns the results of 'projecting' this feature onto another
slice . This is useful to see where a feature
would lie in a coordinate system in which it
crosses a boundary.
This method returns a reference to a list of
Bio::EnsEMBL::ProjectionSegment objects.
ProjectionSegments are blessed arrays and can also be used as
triplets [from_start,from_end,to_Slice]. The from_start and
from_end are the coordinates relative to the feature start.
For example, if a feature is current 100-200bp on a slice
then the triplets returned might be:
[1,50,$slice1],
[51,101,$slice2]
The to_Slice is a slice spanning the region on the requested
coordinate system that this feature projected to.
If the feature projects entirely into a gap then a reference to
an empty list is returned.
Returntype : listref of Bio::EnsEMBL::ProjectionSegments
which can also be used as [$start,$end,$slice] triplets
Exceptions : slice does not have an adaptor
Caller : general
Status : At Riskproject
Arg [1] : string $name
The name of the coordinate system to project this feature onto
Arg [2] : string $version (optional)
The version of the coordinate system (such as 'NCBI34') to
project this feature onto
Example :
my $clone_projection = $feature->project('clone');
foreach my $seg (@$clone_projection) {
my $clone = $seg->to_Slice();
print "Features current coords ", $seg->from_start, '-',
$seg->from_end, " project onto clone coords " .
$clone->seq_region_name, ':', $clone->start, '-', $clone->end,
$clone->strand, "\n";
}
Description: Returns the results of 'projecting' this feature onto another
coordinate system. This is useful to see where a feature
would lie in a coordinate system in which it
crosses a boundary.
This method returns a reference to a list of
Bio::EnsEMBL::ProjectionSegment objects.
ProjectionSegments are blessed arrays and can also be used as
triplets [from_start,from_end,to_Slice]. The from_start and
from_end are the coordinates relative to the feature start.
For example, if a feature is current 100-200bp on a slice
then the triplets returned might be:
[1,50,$slice1],
[51,101,$slice2]
The to_Slice is a slice spanning the region on the requested
coordinate system that this feature projected to.
If the feature projects entirely into a gap then a reference to
an empty list is returned.
Returntype : listref of Bio::EnsEMBL::ProjectionSegments
which can also be used as [$start,$end,$slice] triplets
Exceptions : slice does not have an adaptor
Caller : general
Status : Stableseqname
Arg [1] : (optional) $seqname
Example : $seqname = $feat->seqname();
Description: Getter/Setter for the name of the sequence that this feature
is on. Normally you can get away with not setting this value
and it will default to the name of the slice on which this
feature is on. It is useful to set this value on features which
do not ordinarily sit on features such as ProteinFeatures which
sit on peptides.
Returntype : string
Exceptions : none
Caller : general
Status : Stabledisplay_id
Arg [1] : none
Example : print $f->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. It is overridden by subclasses to
return an appropriate value for objects of that particular
class. If no appropriate display id is available an empty
string is returned instead.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stableversion
Arg [1] : none
Example : print $f->version();
Description: This method returns a string that is considered to be
the identifier version. It is overridden by subclasses to
return an appropriate value for objects of that particular
class. If no appropriate version is available an empty
string is returned instead.
Returntype : string
Exceptions : none
Caller : general
Status : Stablefeature_Slice
Args : none
Example : $slice = $feature->feature_Slice()
Description: This is a convenience method to return a slice that covers the
Area of this feature. The feature start will be at 1 on it, and
it will have the length of this feature.
Returntype : Bio::EnsEMBL::Slice or undef if this feature has no attached
Slice.
Exceptions : warning if Feature does not have attached slice.
Caller : web drawing code
Status : Stableseq_region_name
Arg [1] : none
Example : print $feature->seq_region_name();
Description: Gets the name of the seq_region which this feature is on.
Returns undef if this Feature is not on a slice.
Returntype : string or undef
Exceptions : none
Caller : general
Status : Stableseq_region_length
Arg [1] : none
Example : print $feature->seq_region_length();
Description: Returns the length of the seq_region which this feature is on
Returns undef if this Feature is not on a slice.
Returntype : int (unsigned) or undef
Exceptions : none
Caller : general
Status : Stableseq_region_strand
Arg [1] : none
Example : print $feature->seq_region_strand();
Description: Returns the strand of the seq_region which this feature is on
(i.e. feature_strand * slice_strand)
Returns undef if this Feature is not on a slice.
Returntype : 1,0,-1 or undef
Exceptions : none
Caller : general
Status : Stableseq_region_start
Arg [1] : none
Example : print $feature->seq_region_start();
Description: Convenience method which returns the absolute start of this
feature on the seq_region, as opposed to the relative (slice)
position.
Returns undef if this feature is not on a slice or slice is
circular and cannot determine the position of the feature from
the db.
Returntype : int or undef
Exceptions : none
Caller : general
Status : Stableseq_region_end
Arg [1] : none
Example : print $feature->seq_region_end();
Description: Convenience method which returns the absolute end of this
feature on the seq_region, as opposed to the relative (slice)
position.
Returns undef if this feature is not on a slice or slice is
circular and cannot determine the position of the feature from
the db.
Returntype : int or undef
Exceptions : none
Caller : general
Status : Stablecoord_system_name
Arg [1] : none
Example : print $feature->coord_system_name()
Description: Gets the name of the coord_system which this feature is on.
Returns undef if this Feature is not on a slice.
Returntype : string or undef
Exceptions : none
Caller : general
Status : Stableseq
Args : none
Example : my $dna_sequence = $simple_feature->seq();
Description: Returns the dna sequence from the attached slice and
attached database that overlaps with this feature.
Returns undef if there is no slice or no database.
Returns undef if this feature is unstranded (i.e. strand=0).
Returntype : String or undef
Exceptions : warning if this feature is not stranded
Caller : general
Status : Stableget_all_alt_locations
Arg [1] : Boolean override flag to force the method to return all
Features on the reference sequence as well.
Example : @features = @{$feature->get_all_alt_locations()};
foreach $f (@features) {
print $f->slice->seq_region_name,' ',$f->start, $f->end,"\n";
}
Description: Retrieves shallow copies of this feature in its alternate
locations. A feature can be considered to have multiple
locations when it sits on a alternative structural haplotype
or when it is on a Pseudo Autosomal Region. Most features will
just return a reference to an empty list though.
The features returned by this method will be on a slice which
covers the entire alternate region.
Currently this method does not take into account alternate
locations on the alternate locations (e.g. a reference
sequence may have multiple alternate haplotypes. Asking
for alternate locations of a feature on one of the alternate
haplotypes will give you back the reference location, but not
locations on the other alternate haplotypes).
Returntype : listref of features of the same type of this feature.
Exceptions : none
Caller : general
Status : Stableoverlaps
Arg [1] : Bio::EnsEMBL::Feature $f
The other feature you want to check overlap with this feature
for.
Description: This method does a range comparison of this feature's C<seq_region_start> and
C<seq_region_end> and compares it with another feature's C<seq_region_start>
and C<seq_region_end>. It will return true if these ranges overlap
and the features are on the same seq_region.
For local coordinate overlaps tests (those values returned from
start and end) use C<overlaps_local()>.
Returntype : TRUE if features overlap, FALSE if they don't
Exceptions : warning if features are on different seq_regions
Caller : general
Status : Stableoverlaps_local
Arg [1] : Bio::EnsEMBL::Feature $f
The other feature you want to check overlap with this feature
for.
Description: This method does a range comparison of this feature's start and
end and compares it with another feature's start and end. It
will return true if these ranges overlap and the features are
on the same seq_region.
This method will not attempt to resolve starts and ends with
reference to the feature's backing Slice.
For global coordinate overlaps tests (with reference to the feature's
backing sequence region) use C<overlaps()>.
Returntype : TRUE if features overlap, FALSE if they don't
Exceptions : warning if features are on different seq_regions
Caller : general
Status : Stableget_overlapping_Genes Arg [1] : Optional Boolean: Stranded match i.e. match strand of Feature and Genes Arg [2] : Optional Boolean: Get Genes with an overlapping 5' end Arg [3] : Optional Boolean: Get Genes with an overlapping 3' end Description: Get all the genes that overlap this feature. Returntype : list ref of Bio::EnsEMBL::Gene Caller : general Status : UnStable
get_nearest_Gene
Description: Get the nearest genes to the feature
Returntype : Bio::EnsEMBL::Gene or undef if none can be found nearby
Caller : general
Status : At riskfeature_so_acc
Description: This method returns a string containing the SO accession number of the feature
Define constant SEQUENCE_ONTOLOGY in classes that require it, or override it for multiple possible values for a class.
Returntype : String (Sequence Ontology accession number)
Exceptions : Thrown if caller SEQUENCE_ONTOLOGY is undefined and is not a Bio::EnsEMBL::Featurefeature_so_term
Description: This method returns a string containing the SO term of the feature
Define constant SEQUENCE_ONTOLOGY in classes that require it, or override it for multiple possible values for a class.
Returntype : String (Sequence Ontology term)
Exceptions : Thrown if caller SEQUENCE_ONTOLOGY is undefined and is not a Bio::EnsEMBL::Featuresummary_as_hash
Example : $feature_summary = $feature->summary_as_hash();
Description : Retrieves a textual summary of this Feature.
Should be overidden by subclasses for specific tweaking
Returns : hashref of arrays of descriptive strings
Status : Intended for internal usespecies
Example : $feature->species();
Description : Shortcut to the feature's DBAdaptor and returns its species name
Returntype : String the species name
Exceptions : Thrown if there is no attached adaptor
Caller : Webcodesub_SeqFeature
Deprecated - For genebuild backwards compatibility.
Avoid using it if possibleadd_sub_SeqFeature
Deprecated - only for genebuild backward compatibility.
Avoid using it if possibleflush_sub_SeqFeature
Deprecated - Only for genebuild backwards compatibility.
Avoid using it if possible