Raw content of Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptExtended
<![CDATA[#
# Ensembl module for Bio::EnsEMBL::Analysis::Runnable
#
# Copyright (c) 2006 Ensembl
#
# written by Jan-Hinnerk Vogel
#
#
=head1 NAME
Bio::EnsEMBL::Analysis:Tools::GeneBuildUtils::TranscriptExtended;
=head1 SYNOPSIS
Creation by re-blessing:
for my $t ( @transcripts ) {
bless $t,"Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptExtended";
$t->ev_set('est') ;
}
Creation without re-blessing :
my $tran = new Bio::EnsEMBL::Transcript(-EXONS => \@exons);
=head1 DESCRIPTION
This module extends a Bio::EnsEMBL::Transcript with smoe other
methods. You have to re-bless your Bio::EnsEMBL::Transcript objects
to use it.
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptExtended;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Feature ;
use Bio::EnsEMBL::Transcript ;
use Bio::EnsEMBL::Utils::Exception qw(throw warning );
@ISA = qw(Bio::EnsEMBL::Transcript Bio::EnsEMBL::Feature);
sub new {
my($class) = shift;
if( ref $class ) {
$class = ref $class;
}
my $self = $class->SUPER::new(@_);
return $self ;
$self->{different_est_support} = {} ;
}
=head
Name : ev_set
Arg : String
Func : getter/setter for the evidence-set
Return : String describing ev_set (defined in GeneBuild/TrancriptCoalescer.pm)
=cut
sub ev_set {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'set'} = $value;
}
return $self->{'set'};
}
=head
Name : remove_Exon
Arg : Bio::EnsEMBL::Exon
Func : removes exon from Bio::EnsEMBL::Transcript
Return : none
Example : $transcript->remove_Exon($exon) ;
=cut
sub remove_Exon {
my ($self,$ex_to_remove ) = @_;
unless ($ex_to_remove){
throw ("you have to supply an Bio::EnsEMBL::Exon object ".
"which will be removed from the transcript\n");
}
my $clone=[] ;
my $ea = $self->{'_trans_exon_array'};
my $nr_before = scalar(@$ea);
for my $e (@$ea) {
if ($e ne $ex_to_remove ) {
push @$clone, $e;
}
}
$self->{'_trans_exon_array'} = $clone;
if ($nr_before == scalar(@$clone) ) {
warning( "No matching exon found, exon could not be removed\n" );
}
return ;
}
sub has_3prim_support {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'has_3prim_sup'} = $value;
}
return $self->{'has_3prim_sup'};
}
sub has_5prim_support {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'has_5prim_sup'} = $value;
}
return $self->{'has_5prim_sup'};
}
sub extend_3prim_end {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'extend_3prim_end'} = $value;
}
return $self->{'extend_3prim_end'};
}
sub extend_5prim_end {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'extend_5prim_end'} = $value;
}
return $self->{'extend_5prim_end'};
}
sub nr_exons_overlapped_by_est {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'nr_exons_overlapped_est'}+= $value;
}
return $self->{'nr_exons_overlapped_est'};
}
=head
Name : different_est_support($transcript)
Arg : Bio::EnsEMBL::Transcript
Func : checks if $transcript is not overlapping the other transcripts,
if there is no overlap between already stored transcripts this transcript is added
=cut
sub different_est_support {
my ($self,$new_tr) = @_;
my $overlap ;
if ($new_tr) {
for my $key ( keys %{ $self->{different_est_support} } ) {
my $stored_tr = $self->{different_est_support}{$key} ;
if ($stored_tr->seq_region_start <= $new_tr->seq_region_end &&
$new_tr->seq_region_start <= $stored_tr->seq_region_end ) {
# new_tr overlaps stored_tr
# check which transcript has more exons
my $new_tr_exons = scalar ( @{ $new_tr->get_all_Exons } ) ;
my $stored_tr_exons = scalar(@{$self->{different_est_support}{$stored_tr}->get_all_Exons });
if ($new_tr_exons > $stored_tr_exons ) {
delete $self->{different_est_support}{$stored_tr} ;
if (exists $self->{different_est_support}{$stored_tr}) {
throw(" key wasn't delted\n" ) ;
}else {
warn(" key is deleted\n" ) ;
}
$self->{different_est_support}{$new_tr} = $new_tr ;
}
}else {
${$self->{different_est_support}}{$new_tr}=$new_tr ;
}
}
}
return $self->{different_est_support} ;
}
=head
Name : exchange_exon
Arg[1] : Bio::EnsEMBL::Exon
Arg[2] : Bio::EnsEMBL::Exon
Func : splices a new exon in a Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptExtended-object
and cut's ond the old Bio::EnsEMBL::Exon object
Returnval : Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptExtended()
=cut
sub exchange_exon {
my ($self, $old_exon, $new_exon ) = @_ ;
my $biotype = $self->biotype ;
my @exons = @{ $self->get_all_Exons } ;
my $new_tr = Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils::TranscriptExtended->new();
for my $e (@exons) {
if ($e eq $old_exon) {
$e = $new_exon ;
}
$new_tr->add_Exon($e) ;
}
$new_tr->biotype($biotype) ;
return $new_tr ;
}
=head
Name : score
Arg[1] : Scalar score
Func : Get / Set a score value for the transcript
Returnval : Scalar score
=cut
sub score {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'score'} = $value;
}
return $self->{'score'};
}
=head
Name : similarity
Arg[1] : Bio::EnsEMBL::Transcript
Func : Get / Set a similarity transcript associated with this transcript
Returnval : Bio::EnsEMBL::Transcript
=cut
sub similarity {
my ($self,$value) = @_;
if (defined($value)) {
$self->{'similarity'} = $value;
}
return $self->{'similarity'};
}
1;
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