=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] 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. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut =head1 NAME Bio::EnsEMBL::PredictionExon - A class representing an Exon from an ab initio prediction method =head1 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(); =head1 DESCRIPTION This is a class which represents an prediction exon which is part of a predcition transcript. See Bio::EnsEMBL:PredictionTranscript =head1 METHODS =cut package Bio::EnsEMBL::PredictionExon; use vars qw(@ISA); use strict; use Bio::EnsEMBL::Feature; use Bio::EnsEMBL::Exon; use Bio::EnsEMBL::Utils::Exception qw( warning throw ); use Bio::EnsEMBL::Utils::Argument qw( rearrange ); @ISA = qw(Bio::EnsEMBL::Exon); =head2 new Args : see SUPERCLASS Bio::EnsEMBL::Exon Example : none Description: create an Exon object Returntype : Bio::EnsEMBL::PredictionExon Exceptions : none Caller : general Status : Stable =cut sub new { my $class = shift; $class = ref $class || $class; my $self = $class->SUPER::new( @_ ); my ( $p_value, $score ) = rearrange( [ "P_VALUE", "SCORE" ], @_ ); $self->{'p_value'} = $p_value; $self->{'score'} = $score; return $self; } =head2 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 =cut sub score{ my $self = shift; $self->{'score'} = shift if(@_); return $self->{'score'}; } =head2 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 =cut sub p_value{ my $self = shift; $self->{'p_value'} = shift if(@_); return $self->{'p_value'}; } =head2 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 =cut sub end_phase { my $self = shift; if( @_ ) { throw( "End_phase setting not supported" ); } return ($self->phase() + $self->length()) % 3; } =head2 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 =cut sub transform { my $self = shift; # catch for old style transform calls if( !@_ || ( ref $_[0] && ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" )))) { throw( "transform needs coordinate systems details now," . "please use transfer" ); } my $new_exon = Bio::EnsEMBL::Feature::transform( $self, @_ ); return undef unless $new_exon; #dont want to share the same sequence cache delete $new_exon->{'_seq_cache'}; return $new_exon; } =head2 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 =cut sub transfer { my $self = shift; my $new_exon = Bio::EnsEMBL::Feature::transfer( $self, @_ ); return undef unless $new_exon; #dont want to share the same sequence cache delete $new_exon->{'_seq_cache'}; return $new_exon; } =head2 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 =cut sub summary_as_hash { my $self = shift; my $summary_ref = $self->SUPER::summary_as_hash; delete $summary_ref->{'constitutive'}; delete $summary_ref->{'ensembl_phase'}; delete $summary_ref->{'ensembl_end_phase'}; $summary_ref->{'Parent'} = $self->transcript->dbID() if $self->transcript(); $summary_ref->{'source'} = $self->prediction_transcript->analysis->gff_source() || 'ensembl'; return $summary_ref; } =head2 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 =cut sub transcript { my $self = shift; return $self->prediction_transcript; } =head2 prediction_transcript Example : $prediction_transcript = $exon->prediction_transcript; Description : Locates the parent prediction transcript using an exon dbID Returns : Bio::EnsEMBL::PredictionTranscript =cut sub prediction_transcript{ my $self = shift; my $prediction_transcript_adaptor = $self->adaptor->db->get_PredictionTranscriptAdaptor(); my $parent_prediction_transcript = $prediction_transcript_adaptor->fetch_by_prediction_exon_id($self->dbID); return $parent_prediction_transcript; } =head2 add_supporting_features Description: For compatibility with Bio::EnsEMBL::Exon Does nothing. Returntype : none Status : Stable =cut sub add_supporting_features { } =head2 get_all_supporting_features Description: For compatibility with Bio::EnsEMBL::Exon Does nothing and returns empty list Returntype : empty list. Status : Stable =cut sub get_all_supporting_features { return []; } =head2 find_supporting_evidence Description: For compatibility with Bio::EnsEMBL::Exon Does nothing. Returntype : empty list. Status : Stable =cut sub find_supporting_evidence { return []; } 1;