Raw content of Bio::EnsEMBL::Utils::Converter::bio_ens
<![CDATA[=head1 LICENSE
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
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=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
package Bio::EnsEMBL::Utils::Converter::bio_ens;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Analysis;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Utils::Converter;
@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);
$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
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;
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