Bio::EnsEMBL::Utils::Converter
bio_ens_gene
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Summary
Bio::EnsEMBL::Utils::Converter::bio_ens_gene
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
No synopsis!
Description
This module is to convert from objects of
Bio::SeqFeature::Gene::GeneStructure to those of Bio::EnsEMBL::Gene
Methods
_convert_single | No description | Code |
_initialize | No description | Code |
Methods description
None available.
Methods code
_convert_single | description | prev | next | Top |
sub _convert_single
{ my ($self, $input) = @_;
unless($input->isa('Bio::SeqFeature::Gene::GeneStructure')){
$self->throw("a Bio::SeqFeature::Gene::GeneStructure object needed");
}
my $gene = $input;
my $ens_gene = Bio::EnsEMBL::Gene->new();
$ens_gene->analysis($self->analysis);
my @transcripts = $gene->transcripts;
$self->{_converter_for_transcripts}->contig($self->contig);
$self->{_converter_for_transcripts}->analysis($self->analysis);
my $ens_transcripts = $self->{_converter_for_transcripts}->convert(\@
transcripts);
foreach(@{$ens_transcripts}){
$ens_gene->add_Transcript($_);
}
return $ens_gene;
}
1; } |
sub _initialize
{ my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
$self->{_converter_for_transcripts} = new Bio::EnsEMBL::Utils::Converter(
-in => 'Bio::SeqFeature::Gene::Transcript',
-out => 'Bio::EnsEMBL::Transcript'
); } |
General documentation
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html