——=head1 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
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 <http://lists.ensembl.org/mailman/listinfo/dev>.
Questions may also be sent to the Ensembl help desk at
=head1 AUTHOR
Juguang Xiao <juguang@tll.org.sg>
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Converter::bio_ens_transcript - the instance converter
=head1 SYNOPISIS
=head1 DESCRIPTION
=head1 METHODS
=cut
$Bio::EnsEMBL::Utils::Converter::bio_ens_transcript::VERSION
=
'112.0.0_57'
;
# TRIAL
$Bio::EnsEMBL::Utils::Converter::bio_ens_transcript::VERSION
=
'112.0.057'
;
use
strict;
@ISA
=
qw(Bio::EnsEMBL::Utils::Converter::bio_ens)
;
sub
_convert_single {
my
(
$self
,
$arg
) =
@_
;
unless
(
$arg
->isa(
'Bio::SeqFeature::Gene::Transcript'
)){
$self
->throw(
"A Bio::SeqFeature::Gene::Transcript object needed"
);
}
my
$transcript
=
$arg
;
my
@exons
=
$transcript
->exons_ordered;
$self
->{_converter_for_exons}->contig(
$self
->contig);
$self
->{_converter_for_exons}->analysis(
$self
->analysis);
my
$ens_exons
=
$self
->{_converter_for_exons}->convert(\
@exons
);
my
$ens_transcript
= Bio::EnsEMBL::Transcript->new(@{
$ens_exons
});
$ens_transcript
->start(
$transcript
->start);
$ens_transcript
->end(
$transcript
->end);
# $ens_transcript->strand($transcript->strand);
return
$ens_transcript
;
}
sub
_initialize {
my
(
$self
,
@args
) =
@_
;
$self
->SUPER::_initialize(
@args
);
$self
->{_converter_for_exons} = new Bio::EnsEMBL::Utils::Converter(
-in
=>
'Bio::SeqFeature::Gene::Exon'
,
-out
=>
'Bio::EnsEMBL::Exon'
);
}