my $self = shift;
my $new_transcript = $self->SUPER::transform(@_);
if ( !defined($new_transcript) ) {
my @segments = @{ $self->
project(@_) };
# if it projects, maybe the exons transform well?
# lazy load them here
if ( !@segments ) {
return undef;
}
$self->get_all_Exons();
}
if( exists $self->{'_trans_exon_array'} ) {
my @new_exons;
my ( $low_start, $hi_end, $slice );
# we want to check whether the transform preserved 5prime 3prime
# ordering. This assumes 5->3 order. No complaints on transsplicing.
my ( $last_new_start, $last_old_strand,
$last_new_strand, $start_exon, $end_exon,
$last_seq_region_name );
my $first = 1;
my $ignore_order = 0;
my $order_broken = 0;
for my $old_exon ( @{$self->{'_trans_exon_array'}} ) {
my $new_exon = $old_exon->transform( @_ );
return undef if( !defined $new_exon );
if( ! defined $new_transcript ) {
if( !$first ) {
if( $old_exon->strand() != $last_old_strand ) {
# transsplicing, ignore ordering
$ignore_order = 1;
}
if( $new_exon->slice()->seq_region_name() ne
$last_seq_region_name ) {
return undef;
}
if( $last_new_strand == 1 and
$new_exon->start() < $last_new_start ) {
$order_broken = 1;
}
if( $last_new_strand == -1 and
$new_exon->start() > $last_new_start ) {
$order_broken = 1;
}
#additional check that if exons were on same strand previously, they should be again
if(($last_old_strand == $old_exon->strand()) and !($last_new_strand == $new_exon->strand())){
return undef;
}
if( $new_exon->start() < $low_start ) {
$low_start = $new_exon->start();
}
if( $new_exon->end() > $hi_end ) {
$hi_end = $new_exon->end();
}
} else {
$first = 0;
$low_start = $new_exon->start();
$hi_end = $new_exon->end();
}
$last_seq_region_name = $new_exon->slice()->seq_region_name();
$last_old_strand = $old_exon->strand();
$last_new_start = $new_exon->start();
$last_new_strand = $new_exon->strand();
}
if( defined $self->{'translation'} ) {
if( $self->translation()->start_Exon() == $old_exon ) {
$start_exon = $new_exon;
}
if( $self->translation()->end_Exon() == $old_exon ) {
$end_exon = $new_exon;
}
}
push( @new_exons, $new_exon );
}
if( $order_broken && !$ignore_order ) {
warning( "Order of exons broken in transform of ".$self->dbID() );
return undef;
}
if( !defined $new_transcript ) {
%$new_transcript = %$self;
bless $new_transcript, ref( $self );
$new_transcript->start( $low_start );
$new_transcript->end( $hi_end );
$new_transcript->slice( $new_exons[0]->
slice() );
$new_transcript->strand( $new_exons[0]->
strand() );
}
$new_transcript->{'_trans_exon_array'} = \@new_exons;
# should be ok to do inside exon array loop
# translations only exist together with the exons ...
if( defined $self->{'translation'} ) {
my $new_translation;
%$new_translation = %{$self->{'translation'}};;
bless $new_translation, ref( $self->{'translation'} );
$new_transcript->{'translation'} = $new_translation;
$new_translation->start_Exon( $start_exon );
$new_translation->end_Exon( $end_exon );
}
}
if( exists $self->{'_supporting_evidence'} ) {
my @new_features;
for my $old_feature ( @{$self->{'_supporting_evidence'}} ) {
my $new_feature = $old_feature->transform( @_ );
if (defined $new_feature) {
push @new_features, $new_feature;
}
}
$new_transcript->{'_supporting_evidence'} = \@new_features;
}
if(exists $self->{_ise_array}) {
my @new_features;
foreach my $old_feature ( @{$self->{_ise_array}} ) {
my $new_feature = $old_feature->transform(@_);
push( @new_features, $new_feature );
}
$new_transcript->{_ise_array} = \@new_features;
}
if(exists $self->{attributes}) {
$new_transcript->{attributes} = [@{$self->{attributes}}];
}
# flush cached internal values that depend on the exon coords
$new_transcript->{'transcript_mapper'} = undef;
$new_transcript->{'coding_region_start'} = undef;
$new_transcript->{'coding_region_end'} = undef;
$new_transcript->{'cdna_coding_start'} = undef;
$new_transcript->{'cdna_coding_end'} = undef;
return $new_transcript;
}
Inheritance diagram for Bio::EnsEMBL::Transcript:
