=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
Questions may also be sent to the Ensembl help desk at
=head1 AUTHOR
Juguang Xiao <juguang@fugu-sg.org>
=cut
=head1 NAME
Bio::EnsEMBL::Utils::Converter::bio_ens
=head1 SYNOPISIS
You should not use this module directly. Please check out the
Bio::EnsEMBL::Utils::Converter module.
=head1 DESCRIPTION
=head1 METHODS
=cut
$Bio::EnsEMBL::Utils::Converter::bio_ens::VERSION = '112.0.0';
use strict;
use vars qw(@ISA);
use Scalar::Util qw(weaken);
@ISA = qw(Bio::EnsEMBL::Utils::Converter);
=head2 new
Please see Bio::EnsEMBL::Utils::Converter::new
=cut
sub new {
my ($caller, @args) = @_;
my $class = ref($caller) || $caller;
if($class eq 'Bio::EnsEMBL::Utils::Converter::bio_ens'){
my %params = @args;
@params{map{lc $_} keys %params} = values %params;
my $module = $class->_guess_module($params{-in}, $params{-out});
return undef unless ($class->_load_module($module));
return "$module"->new(@args);
}else{
my $self = $class->SUPER::new(@args);
# $self->_initialize(@args);
return $self;
}
}
sub _initialize {
my ($self, @args) = @_;
$self->SUPER::_initialize(@args);
my ($dbadaptor,
$dbdriver, $dbhost, $dbport, $dbuser, $dbpass, $dbname,
$analysis, $analysis_dbid, $analysis_logic_name,
$contig, $contig_dbid, $contig_name,
$translation_id) =
$self->_rearrange([qw(DBADAPTOR
DBDRIVER DBHOST DBPORT DBUSER DBPASS DBNAME
ANALYSIS ANALYSIS_DBID ANALYSIS_LOGIC_NAME
CONTIG CONTIG_DBID CONTIG_NAME
TRANSLATION_ID)], @args);
if(defined $dbadaptor){
$self->dbadaptor($dbadaptor);
}elsif(defined $dbname){
$self->ensembl_db(@args);
}else{
# No db information.
}
if(defined $analysis){
$self->analysis($analysis);
# then ignore the analysis_dbid and analysis_logic_name
}elsif(defined $analysis_dbid){
$self->analysis_dbID($analysis_dbid);
}elsif(defined $analysis_logic_name){
$self->analysis_logic_name($analysis_logic_name);
}else{
# No analysis information offered
}
if(defined $contig){
($contig) = ref($contig) eq 'ARRAY' ? @{$contig} : $contig;
$self->contig($contig);
}elsif(defined $contig_dbid){
$self->contig_dbID($contig_dbid);
}elsif(defined $contig_name){
$self->contig_name($contig_name);
}else{
# No contig information
}
if(defined $translation_id){
$self->translation_id($translation_id);
}
}
sub _guess_module {
my ($self, $in, $out) = @_;
my $tail;
if($in eq 'Bio::Search::HSP::GenericHSP'){
$tail = 'bio_ens_hsp';
}elsif($in eq 'Bio::SeqFeature::Generic'){
$tail = 'bio_ens_seqFeature';
}elsif($in eq 'Bio::SeqFeature::FeaturePair'){
$tail = 'bio_ens_featurePair';
}elsif($in eq 'Bio::Pipeline::Analysis'){
$tail = 'bio_ens_analysis';
}elsif($in eq 'Bio::Tools::Prediction::Gene'){
$tail = 'bio_ens_predictionGene';
}elsif($in eq 'Bio::Tools::Prediction::Exon'){
$tail = 'bio_ens_predictionExon';
}elsif($in eq 'Bio::SeqFeature::Gene::GeneStructure'){
$tail = 'bio_ens_gene';
}elsif($in eq 'Bio::SeqFeature::Gene::Transcript'){
$tail = 'bio_ens_transcript';
}elsif($in eq 'Bio::SeqFeature::Gene::Exon'){
$tail = 'bio_ens_exon';
}else{
$self->throw("[$in] to [$out], not supported");
}
return "Bio::EnsEMBL::Utils::Converter::$tail";
}
=head2 analysis
Title : analysis
Usage : $self->analysis
Function: get and set for analysis
Return : L<Bio::EnsEMBL::Analysis>
Args : L<Bio::EnsEMBL::Analysis>
=cut
sub analysis {
my ($self, $arg) = @_;
if(defined($arg)){
# convert the analysis, if it's not Bio::Pipeline::Analysis
if($arg->isa('Bio::Pipeline::Analysis')){
my $converter_for_analysis = new Bio::EnsEMBL::Utils::Converter(
-in => 'Bio::Pipeline::Analysis',
-out => 'Bio::EnsEMBL::Analysis'
);
($arg) = @{ $converter_for_analysis->convert([$arg]) };
}
$self->throws("A Bio::EnsEMBL::Analysis object expected.")
unless($arg->isa('Bio::EnsEMBL::Analysis'));
$self->{_analysis} = $arg;
$self->{_analysis_dbid} = $arg->dbID;
$self->{_analysis_logic_name} = $arg->logic_name;
}
return $self->{_analysis};
}
=head2 contig
Title : contig
Usage : $self->contig
Function: get and set for contig
Return :
Args :
=cut
sub contig {
my ($self, $arg) = @_;
if(defined($arg)){
if($arg->isa('Bio::EnsEMBL::RawContig')){
$self->{_contig_dbid} = $arg->dbID;
$self->{_contig_name} = $arg->name;
}elsif($arg->isa('Bio::EnsEMBL::Slice')){
$self->{_slice_dbid} = $arg->dbID;
}elsif($arg->isa('Bio::PrimarySeqI')){
;
}else{
$self->throw("a Bio::EnsEMBL::RawContig needed");
}
$self->{_contig} = $arg;
}
return $self->{_contig};
}
=head2 dbadaptor
Title : dbadaptor
Usage : $self->dbadaptor
Function: get and set for dbadaptor
Return : L<Bio::EnsEMBL::DBSQL::DBAdaptor>
Args : L<Bio::EnsEMBL::DBSQL::DBAdaptor>
=cut
sub dbadaptor {
my ($self, $arg) = @_;
if(defined($arg)){
$self->throws("A Bio::EnsEMBL::DBSQL::DBAdaptor object expected.") unless(defined $arg);
weaken($self->{_dbadaptor} = $arg);
}
return $self->{_dbadaptor};
}
=head2 ensembl_db
Title : ensembl_db
Usage :
Function:
Return :
Args :
=cut
sub ensembl_db {
my ($self, @args) = @_;
my ($dbdriver, $dbhost, $dbport, $dbuser, $dbpass, $dbname) = $self->_rearrange(
[qw(DBDRIVER DBHOST DBPORT DBUSER DBPASS DBNAME)], @args);
my $dbadaptor = new Bio::EnsEMBL::DBSQL::DBAdaptor(
-driver => $dbdriver,
-host => $dbhost,
-port => $dbport,
-user => $dbuser,
-pass => $dbpass,
-dbname => $dbname
);
$self->dbadaptor($dbadaptor);
}
=head2 analysis_dbID
Title : analysis_dbID
Usage :
Function:
Return :
Args :
=cut
sub analysis_dbID {
my ($self, $arg) = @_;
if(defined $arg){
my $analysis;
eval{
$analysis = $self->dbadaptor->get_AnalysisAdaptor->fetch_by_dbID($arg);
};
$self->throw("Failed during fetching analysis by dbID\n$@") if($@);
$self->analysis($analysis);
}
$self->{_analysis_dbid};
}
=head2 analysis_logic_name
Title : analysis_logic_name
Usage :
Function:
Return :
Args :
=cut
sub analysis_logic_name {
my ($self, $arg) = @_;
return $self->{_analysis_logic_name} unless(defined $arg);
my $analysis;
eval{
$analysis =
$self->dbadaptor->get_AnalysisAdaptor->fetch_by_logic_name($arg);
};
$self->throw("Not found analysis with logic name as \[$arg\]\n$@") if($@);
$self->analysis($analysis);
return $self->{_analysis_logic_name};
}
=head2 contig_dbID
Title : contig_dbID
Usage : $self->contig_dbID
Function: get and set for contig_dbID
Return :
Args :
=cut
sub contig_dbID {
my ($self, $arg) = @_;
if(defined($arg)){
my $contig;
eval{
$contig =
$self->dbadaptor->get_RawContigAdaptor->fetch_by_dbID($arg);
};
$self->throw("Failed during fetching contig by dbID\n$@") if($@);
$self->contig($contig);
}
return $self->{_contig_dbid};
}
=head2 contig_name
Title : contig_name
Usage : $self->contig_name
Function: get and set for contig_name
Return :
Args :
=cut
sub contig_name {
my ($self, $arg) = @_;
if(defined($arg)){
my $contig;
eval{
$contig =
$self->dbadaptor->get_RawContigAdaptor->fetch_by_name($arg);
};
$self->throw("Failed during fetching contig by dbID\n$@") if($@);
$self->contig($contig);
}
return $self->{_contig_name};
}
=head2 slice_dbID
Title : slice
Usage : $self->slice
Function: get and set for slice
Return : L<Bio::EnsEMBL::Slice>
Args : L<Bio::EnsEMBL::Slice>
=cut
sub slice_dbID {
my ($self, $arg) = @_;
if(defined($arg)){
my $slice;
$self->throw("undefined dbadpator") unless defined $self->dbadpaotr;
eval{
my $sliceAdaptor = $self->dbadaptor->get_SliceAdaptor;
$slice = $sliceAdaptor->fetch_by_dbID($arg);
};
$self->throw("Failed to fetch slice by dbID\n$@") if($@);
$self->contig($slice);
}
}
=head2 slice_chr_start_end
Title : slice_chr_start_end
Usage : my $slice = $self->slice_chr_start_end($chr, $start, $end);
Function: get and set for slice_chr_start_end
Return :
Args :
=cut
sub slice_chr_start_end {
my ($self, $chr, $start, $end) = @_;
if(defined($chr) && defined($start) && defined($end)){
my $slice;
eval{
my $sliceAdaptor = $self->dbadaptor->get_SliceAdaptor;
$slice = $sliceAdaptor->fetch_by_chr_start_end($chr, $start, $end);
};
$self->throw("Failed to fetch slice by chr start end\n$@") if($@);
$self->contig($slice);
}
}
sub translation_id {
my ($self, $arg) = @_;
return $self->{_translation_id} = $arg if(defined($arg));
return $self->{_translation_id};
}
1;