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Bio-EnsEMBL-112.0.0
River stage zero No dependents
/ Bio::EnsEMBL::PredictionExon

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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NAME

Bio::EnsEMBL::PredictionExon - A class representing an Exon from an ab initio prediction method

SYNOPSIS

$exon = new Bio::EnsEMBL::PredictionExon(
  -START   => 100,
  -END     => 200,
  -STRAND  => 1,
  -SLICE   => $slice,
  -DBID    => $dbID,
  -P_VALUE => 23.5,
  -SCORE   => 99
);

# 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 prediction exon which is part of a predcition transcript. See Bio::EnsEMBL:PredictionTranscript

METHODS

new

Args       : see SUPERCLASS Bio::EnsEMBL::Exon
Example    : none
Description: create an Exon object
Returntype : Bio::EnsEMBL::PredictionExon 
Exceptions : none
Caller     : general
Status     : Stable

score

Arg [1]    : string $newval (optional) 
             The new value to set the score attribute to
Example    : $score = $obj->score()
Description: Getter/Setter for the score attribute
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

p_value

Arg [1]    : string $newval (optional) 
             The new value to set the p_value attribute to
Example    : $p_value = $obj->p_value()
Description: Getter/Setter for the p_value attribute
Returntype : string
Exceptions : none
Caller     : general
Status     : Stable

end_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     : Stable

transform

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     : Stable

transfer

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::Gene
Exceptions : none
Caller     : general
Status     : Stable

summary_as_hash

Example       : $exon_summary = $exon->summary_as_hash();
Description   : Extends Feature::summary_as_hash
                Retrieves a summary of this prediction exon.
Returns       : hashref of descriptive strings
Status        : Intended for internal use

transcript Example : $prediction_transcript = $exon->transcript; Description : Locates the parent prediction transcript using an exon dbID Same as prediction_transcript, duplicated for compatibility with Exon feature Returns : Bio::EnsEMBL::PredictionTranscript

prediction_transcript

Example     : $prediction_transcript = $exon->prediction_transcript;
Description : Locates the parent prediction transcript using an exon dbID
Returns     : Bio::EnsEMBL::PredictionTranscript

add_supporting_features

Description: For compatibility with Bio::EnsEMBL::Exon
             Does nothing.
Returntype : none
Status     : Stable

get_all_supporting_features

Description: For compatibility with Bio::EnsEMBL::Exon
             Does nothing and returns empty list
Returntype : empty list.
Status     : Stable

find_supporting_evidence

Description: For compatibility with Bio::EnsEMBL::Exon
             Does nothing.
Returntype : empty list.
Status     : Stable