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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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Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.NAME
Bio::EnsEMBL::Exon - A class representing an Exon
SYNOPSIS
$exon = new Bio::EnsEMBL::Exon(
-START => 100,
-END => 200,
-STRAND => 1,
-SLICE => $slice,
-DBID => $dbID,
-ANALYSIS => $analysis,
-STABLE_ID => 'ENSE000000123',
-VERSION => 2
);
# seq() returns a Bio::Seq
my $seq = $exon->seq->seq();
# Peptide only makes sense within transcript context
my $pep = $exon->peptide($transcript)->seq();
# Normal feature operations can be performed:
$exon = $exon->transform('clone');
$exon->move( $new_start, $new_end, $new_strand );
print $exon->slice->seq_region_name();DESCRIPTION
This is a class which represents an exon which is part of a transcript. See Bio::EnsEMBL:Transcript
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] : (optional) 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
Arg [-PHASE] : the phase.
Arg [-END_PHASE]: the end phase
Arg [-STABLE_ID]: (optional) the stable id of the exon
Arg [-VERSION] : (optional) the version
Arg [-CREATED_DATE] : (optional) the created date
Arg [-MODIFIED_DATE]: (optional) the last midifeid date
Example : none
Description: create an Exon object
Returntype : Bio::EnsEMBL::Exon
Exceptions : if phase is not valid (i.e. 0,1, 2 -1)
Caller : general
Status : Stableend_phase
Arg [1] : (optional) int $end_phase
Example : $end_phase = $feat->end_phase;
Description: Gets/Sets the end phase of the exon.
end_phase = number of bases from the last incomplete codon of
this exon.
Usually, end_phase = (phase + exon_length)%3
but end_phase could be -1 if the exon is half-coding and its 3
prime end is UTR.
Returntype : int
Exceptions : warning if end_phase is called without an argument and the
value is not set.
Caller : general
Status : Stablephase
Arg [1] : (optional) int $phase
Example : my $phase = $exon->phase;
$exon->phase(2);
Description: Gets/Sets the phase of the exon.
Returntype : int
Exceptions : throws if phase is not (0, 1 2 or -1).
Caller : general
Status : StableGet or set the phase of the Exon, which tells the translation machinery, which makes a peptide from the DNA, where to start.
The Ensembl phase convention can be thought of as "the number of bases of the first codon which are on the previous exon". It is therefore 0, 1 or 2 (or -1 if the exon is non-coding). In ascii art, with alternate codons represented by ### and +++:
Previous Exon Intron This Exon
...------------- -------------...
5' Phase 3'
...#+++###+++### 0 +++###+++###+...
...+++###+++###+ 1 ++###+++###++...
...++###+++###++ 2 +###+++###+++...Here is another explanation from Ewan:
Phase means the place where the intron lands inside the codon - 0 between codons, 1 between the 1st and second base, 2 between the second and 3rd base. Exons therefore have a start phase and a end phase, but introns have just one phase.
frame
Arg [1] : none
Example : $frame = $exon->frame
Description: Gets the frame of this exon
Returntype : int
Exceptions : thrown if an arg is passed
thrown if frame cannot be calculated due to a bad phase value
Caller : general
Status : Stablestart
Arg [1] : int $start (optional)
Example : $start = $exon->start();
Description: Getter/Setter for the start of this exon. The superclass
implmentation is overridden to flush the internal sequence
cache if this value is altered
Returntype : int
Exceptions : none
Caller : general
Status : Stableend
Arg [1] : int $end (optional)
Example : $end = $exon->end();
Description: Getter/Setter for the end of this exon. The superclass
implmentation is overridden to flush the internal sequence
cache if this value is altered
Returntype : int
Exceptions : none
Caller : general
Status : Stablestrand
Arg [1] : int $strand (optional)
Example : $start = $exon->strand();
Description: Getter/Setter for the strand of this exon. The superclass
implmentation is overridden to flush the internal sequence
cache if this value is altered
Returntype : int
Exceptions : none
Caller : general
Status : Stablecdna_start
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript for which cDNA coordinates should be
relative to.
Example : $cdna_start = $exon->cdna_start($transcript);
Description : Returns the start position of the exon in cDNA
coordinates.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer
Exceptions : Throws if the given argument is not a transcript.
Throws if the first part of the exon maps into a gap.
Throws if the exon can not be mapped at all.
Caller : General
Status : Stablecdna_end
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript for which cDNA coordinates should be
relative to.
Example : $cdna_end = $exon->cdna_end($transcript);
Description : Returns the end position of the exon in cDNA
coordinates.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer
Exceptions : Throws if the given argument is not a transcript.
Throws if the last part of the exon maps into a gap.
Throws if the exon can not be mapped at all.
Caller : General
Status : Stablecdna_coding_start
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript for which cDNA coordinates should be
relative to.
Example : $cdna_coding_start = $exon->cdna_coding_start($transcript);
Description : Returns the start position of the coding region of the
exon in cDNA coordinates. Returns undef if the whole
exon is non-coding.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer or undef
Exceptions : Throws if the given argument is not a transcript.
Caller : General
Status : Stablecdna_coding_end
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript for which cDNA coordinates should be
relative to.
Example : $cdna_coding_end = $exon->cdna_coding_end($transcript);
Description : Returns the end position of the coding region of the
exon in cDNA coordinates. Returns undef if the whole
exon is non-coding.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer or undef
Exceptions : Throws if the given argument is not a transcript.
Caller : General
Status : Stablecoding_region_start
Arg [1] : Bio::EnsEMBL::Transcript $transcript
Example : $coding_region_start =
$exon->coding_region_start($transcript);
Description : Returns the start position of the coding region
of the exon in slice-relative coordinates on the
forward strand. Returns undef if the whole exon is
non-coding.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer or undef
Exceptions : Throws if the given argument is not a transcript.
Caller : General
Status : Stablecoding_region_end
Arg [1] : Bio::EnsEMBL::Transcript $transcript
Example : $coding_region_end =
$exon->coding_region_end($transcript);
Description : Returns the end position of the coding region of
the exon in slice-relative coordinates on the
forward strand. Returns undef if the whole exon is
non-coding.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer or undef
Exceptions : Throws if the given argument is not a transcript.
Caller : General
Status : Stablerank
Arg [1] : Bio::EnsEMBL::Transcript $transcript
The transcript for which the exon rank
is requested.
Example : $rank = $exon->rank($transcript);
Description : Returns the rank of the exon relative to
the transcript.
Since an exon may be part of one or more transcripts,
the relevant transcript must be given as argument to
this method.
Return type : Integer
Exceptions : Throws if the given argument is not a transcript.
Throws if the exon does not belong to the transcript.
Caller : General
Status : Stableslice
Arg [1] : Bio::EnsEMBL::Slice
Example : $slice = $exon->slice();
Description: Getter/Setter for the slice this exon is on. The superclass
implmentation is overridden to flush the internal sequence
cache if this value is altered
Returntype : Bio::EnsEMBL::Slice
Exceptions : none
Caller : general
Status : Stableequals
Arg [1] : Bio::EnsEMBL::Exon exon
Example : if ($exonA->equals($exonB)) { ... }
Description : Compares two exons for equality.
The test for eqality goes through the following list
and terminates at the first true match:
1. If Bio::EnsEMBL::Feature::equals() returns false,
then the exons are *not* equal.
2. If both exons have stable IDs: if these are the
same, the exons are equal, otherwise not.
3. If the exons have the same start, end, strand, and
phase, then they are equal, otherwise not.
Return type : Boolean (0, 1)
Exceptions : Thrown if a non-transcript is passed as the argument.move
Arg [1] : int start
Arg [2] : int end
Arg [3] : (optional) int strand
Example : None
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. This overrides the superclass
move() method so that the internal sequence cache can be
flushed if the exon if moved.
Returntype : none
Exceptions : Thrown is invalid arguments are provided
Caller : general
Status : Stabletransform
Arg 1 : String $coordinate_system_name
Arg [2] : String $coordinate_system_version
Description: moves this exon to the given coordinate system. If this exon has
attached supporting evidence, they move as well.
Returntype : Bio::EnsEMBL::Exon
Exceptions : wrong parameters
Caller : general
Status : Stabletransfer
Arg [1] : Bio::EnsEMBL::Slice $destination_slice
Example : none
Description: Moves this Exon to given target slice coordinates. If Features
are attached they are moved as well. Returns a new exon.
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller : general
Status : Stableadd_supporting_features
Arg [1] : Bio::EnsEMBL::Feature $feature
Example : $exon->add_supporting_features(@features);
Description: Adds a list of supporting features to this exon.
Duplicate features are not added.
If supporting features are added manually in this
way, prior to calling get_all_supporting_features then the
get_all_supporting_features call will not retrieve supporting
features from the database.
Returntype : none
Exceptions : throw if any of the features are not Feature
throw if any of the features are not in the same coordinate
system as the exon
Caller : general
Status : Stableflush_supporting_features
Example : $exon->flush_supporting_features;
Description : Removes all supporting evidence from the exon.
Return type : (Empty) listref
Exceptions : none
Caller : general
Status : Stableget_all_supporting_features
Arg [1] : none
Example : @evidence = @{$exon->get_all_supporting_features()};
Description: Retrieves any supporting features added manually by
calls to add_supporting_features. If no features have been
added manually and this exon is in a database (i.e. it has
an adaptor), fetch from the database
Returntype : listreference of Bio::EnsEMBL::BaseAlignFeature objects
Exceptions : none
Caller : general
Status : Stablefind_supporting_evidence
# This method is only for genebuild backwards compatibility. # Avoid using it if possible
Arg [1] : Bio::EnsEMBL::Feature $features
The list of features to search for supporting (i.e. overlapping)
evidence.
Arg [2] : (optional) boolean $sorted
Used to speed up the calculation of overlapping features.
Should be set to true if the list of features is sorted in
ascending order on their start coordinates.
Example : $exon->find_supporting_evidence(\@features);
Description: Looks through all the similarity features and
stores as supporting features any feature
that overlaps with an exon.
Returntype : none
Exceptions : none
Caller : general
Status : Medium Riskstable_id
Arg [1] : string $stable_id
Example : none
Description: get/set for attribute stable_id
Returntype : string
Exceptions : none
Caller : general
Status : Stablecreated_date
Arg [1] : string $created_date
Example : none
Description: get/set for attribute created_date
Returntype : string
Exceptions : none
Caller : general
Status : Stablemodified_date
Arg [1] : string $modified_date
Example : none
Description: get/set for attribute modified_date
Returntype : string
Exceptions : none
Caller : general
Status : Stableversion
Arg [1] : string $version
Example : none
Description: get/set for attribute version
Returntype : string
Exceptions : none
Caller : general
Status : Stablestable_id_version
Arg [1] : (optional) String - the stable ID with version to set
Example : $exon->stable_id("ENSE0000000001.3");
Description: Getter/setter for stable id with version for this exon.
Returntype : String
Exceptions : none
Caller : general
Status : Stableis_current
Arg [1] : Boolean $is_current
Example : $exon->is_current(1)
Description: Getter/setter for is_current state of this exon.
Returntype : Int
Exceptions : none
Caller : general
Status : Stableis_constitutive
Arg [1] : Boolean $is_constitutive
Example : $exon->is_constitutive(0)
Description: Getter/setter for is_constitutive state of this exon.
Returntype : Int
Exceptions : none
Caller : general
Status : Stableis_coding
Arg [1] : Bio::EnsEMBL::Transcript
Example : $exon->is_coding()
Description: Says if the exon is within the translation or not
Returntype : Int
Exceptions : none
Caller : general
Status : Stableadjust_start_end
Arg 1 : int $start_adjustment
Arg 2 : int $end_adjustment
Example : none
Description: returns a new Exon with this much shifted coordinates
Returntype : Bio::EnsEMBL::Exon
Exceptions : none
Caller : Transcript->get_all_translateable_Exons()
Status : Stablepeptide
Arg [1] : Bio::EnsEMBL::Transcript $tr
Example : my $pep_str = $exon->peptide($transcript)->seq;
Description: Retrieves the portion of the transcripts peptide
encoded by this exon. The transcript argument is necessary
because outside of the context of a transcript it is not
possible to correctly determine the translation. Note that
an entire amino acid will be present at the exon boundaries
even if only a partial codon is present. Therefore the
concatenation of all of the peptides of a transcripts exons
is not the same as a transcripts translation because the
summation may contain duplicated amino acids at splice sites.
In the case that this exon is entirely UTR, a Bio::Seq object
with an empty sequence string is returned.
Returntype : Bio::Seq
Exceptions : thrown if transcript argument is not provided
Caller : general
Status : Stable_merge_ajoining_coords
Arg [1] : ArrayRef of Bio::EnsEMBL::Mapper::Coordinate objects
Example :
Description : Merges coords which are ajoining or overlapping
Returntype : Bio::EnsEMBL::Mapper::Coordinate or undef if it cannot happen
Exceptions : Exception if the cooords cannot be condensed into one location
Caller : internal
Status : Developmentseq
Arg [1] : none
Example : my $seq_str = $exon->seq->seq;
Description: Retrieves the dna sequence of this Exon.
Returned in a Bio::Seq object. Note that the sequence may
include UTRs (or even be entirely UTR).
Returntype : Bio::Seq or undef
Exceptions : warning if argument passed,
warning if exon does not have attatched slice
warning if exon strand is not defined (or 0)
Caller : general
Status : Stablehashkey
Arg [1] : none
Example : if(exists $hash{$exon->hashkey}) { do_something(); }
Description: Returns a unique hashkey that can be used to uniquely identify
this exon. Exons are considered to be identical if they share
the same seq_region, start, end, strand, phase, end_phase.
Note that this will consider two exons on different slices
to be different, even if they actually are not.
Returntype : string formatted as slice_name-start-end-strand-phase-end_phase
Exceptions : thrown if not all the necessary attributes needed to generate
a unique hash value are set
set
Caller : general
Status : Stabledisplay_id
Arg [1] : none
Example : print $exons->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For exons this is (depending on
availability and in this order) the stable Id, the dbID or an
empty string.
Returntype : string
Exceptions : none
Caller : web drawing code
Status : Stableload
Args : None
Example : $exon->load();
Description : The Ensembl API makes extensive use of
lazy-loading. Under some circumstances (e.g.,
when copying genes between databases), all data of
an object needs to be fully loaded. This method
loads the parts of the object that are usually
lazy-loaded.
Returns : Nothing.summary_as_hash
Example : $exon_summary = $exon->summary_as_hash();
Description : Extends Feature::summary_as_hash
Retrieves a summary of this Exon.
Returns : hashref of descriptive strings
Status : Intended for internal use