Raw content of Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor
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# Ensembl module for Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor
#
# Copyright (c) 2004 Ensembl
#
# You may distribute this module under the same terms as perl itself
#
#
=head1 NAME
Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor
=head1 SYNOPSIS
# connect to variation database
$vdb = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(...);
# connect to core database
$db = Bio::EnsEMBL::DBSQL::DBAdaptor->new(...);
# tell the variation database where to obtain core database data
$vdb->dnadb($db);
$trva = $vdb->get_TranscriptVariationAdaptor();
$vfa = $vdb->get_VariationFeatureAdaptor();
$tra = $db->get_TranscriptAdaptor();
# retrieve a TranscriptVariation by its internal identifier
$trv = $tra->fetch_by_dbID(552);
print $trv->transcript()->stable_id(), ' ',
$trv->variation_feature()->variation_name(), ' ',
$trv->consequence_type(), "\n";
# retrieve all TranscriptVariations associated with a Transcript
$tr = $tra->fetch_by_stable_id('ENST00000278995');
foreach $trv (@{$trva->fetch_all_by_Transcripts([$tr])}) {
print $trv->variation_feature->variation_name(), ' ', $trv->consequence_type(), "\n";
}
# retrieve all TranscriptVariations associated with a VariationFeature
$vf = $vfa->fetch_by_dbID(99123);
foreach $trv (@{$trva->fetch_all_by_VariationFeatures($vf)}) {
print $trva->transcript->stable_id(), ' ', $trva->consequence_type(), "\n";
}
=head1 DESCRIPTION
This adaptor provides database connectivity for TranscriptVariation objects.
TranscriptVariations which represent an association between a variation and
a Transcript may be retrieved from the Ensembl variation database via several
means using this module.
=head1 AUTHOR - Graham McVicker
=head1 CONTACT
Post questions to the Ensembl development list ensembl-dev@ebi.ac.uk
=head1 METHODS
=cut
use strict;
use warnings;
package Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Variation::TranscriptVariation;
our @ISA = ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
=head2 fetch_all_by_Transcripts
Arg[1] : listref of Bio::EnsEMBL::Transcript
Example : $tr = $ta->fetch_by_stable_id('ENST00000278995');
@tr_vars = @{$tr_var_adaptor->fetch_all_by_Transcripts([$tr])};
Description : Retrieves all TranscriptVariation objects associated with
provided Ensembl Transcript. Attaches them to the TranscriptVariation
ReturnType : ref to list of Bio::EnsEMBL::Variation::TranscriptVariations
Exceptions : throw on bad argument
Caller : general
Status : Stable
=cut
sub fetch_all_by_Transcripts{
my $self = shift;
my $transcript_ref = shift;
if (ref($transcript_ref) ne 'ARRAY' or ! $transcript_ref->[0]->isa('Bio::EnsEMBL::Transcript')){
throw('Array Bio::EnsEMBL::Transcript expected');
}
my %tr_by_id;
foreach my $tr (@{$transcript_ref}) {
if (!$tr->isa('Bio::EnsEMBL::Transcript')){
throw('Bio::EnsEMBL::Transcript is expected');
}
$tr_by_id{$tr->dbID()} = $tr;
}
my $instr = join (",", keys( %tr_by_id));
my $transcript_variations = $self->generic_fetch( "tv.transcript_id in ( $instr )");
for my $tv (@{$transcript_variations}){
#add to the TranscriptVariation object all the Transcripts
$tv->{'transcript'} = $tr_by_id{$tv->{'_transcript_id'}};
delete $tv->{'_transcript_id'}; #remove the transcript_id from the transcript_variation object
}
return $transcript_variations;
}
=head2 fetch_all_by_VariationFeatures
Arg [1] : Bio::EnsEMBL::Variation::VariationFeature $vf
Example :
$vf = $vf_adaptor->fetch_by_dbID(1234);
@tr_vars = @{$tr_var_adaptor->fetch_all_by_VariationFeatures([$vf])});
Description: Retrieves all TranscriptVariation objects associated with
provided Ensembl variation features. Attaches them to the given variation
features.
Returntype : ref to list of Bio::EnsEMBL::Variation::TranscriptVariations
Exceptions : throw on bad argument
Caller : general
Status : Stable
=cut
sub fetch_all_by_VariationFeatures {
my $self = shift;
my $vf_ref = shift;
if(ref($vf_ref) ne 'ARRAY') {
throw('Array Bio::EnsEMBL::Variation::VariationFeature expected');
}
my %vf_by_id;
%vf_by_id = map {$_->dbID(), $_ } @$vf_ref;
my $instr = join (",",keys( %vf_by_id));
my $tvs = $self->generic_fetch( "tv.variation_feature_id in ( $instr )" );
for my $tv ( @$tvs ) {
#add to the variation feature object all the transcript variations
$vf_by_id{ $tv->{'_vf_id'} }->add_TranscriptVariation( $tv );
delete $tv->{'_vf_id'}; #remove the variation_feature_id from the transcript_variation object
}
return $tvs;
}
#
# internal method responsible for constructing transcript variation objects
# from an executed statement handle. Ordering of columns in executed statement
# must be consistant with function implementation.
#
sub _objs_from_sth {
my $self = shift;
my $sth = shift;
my ($trv_id, $tr_id, $vf_id, $cdna_start, $cdna_end, $tl_start, $tl_end,
$pep_allele, $consequence_type);
$sth->bind_columns(\$trv_id, \$tr_id, \$vf_id, \$cdna_start, \$cdna_end,
\$tl_start, \$tl_end, \$pep_allele, \$consequence_type);
my %tr_hash;
my %vf_hash;
my @results;
# construct all of the TranscriptVariation objects
while($sth->fetch()) {
my @consequences = split /,/,$consequence_type;
my $trv = Bio::EnsEMBL::Variation::TranscriptVariation->new_fast
( { 'dbID' => $trv_id,
'adaptor' => $self,
'cdna_start' => $cdna_start,
'cdna_end' => $cdna_end,
'translation_start' => $tl_start,
'translation_end' => $tl_end,
'pep_allele_string' => $pep_allele,
'consequence_type' => \@consequences} );
$trv->{'_vf_id'} = $vf_id; #add the variation feature
$trv->{'_transcript_id'} = $tr_id; #add the transcript id
push @results, $trv;
}
return \@results;
}
sub _tables {return ['transcript_variation','tv'];}
sub _columns {
return qw (tv.transcript_variation_id tv.transcript_id
tv.variation_feature_id tv.cdna_start tv.cdna_end
tv.translation_start tv.translation_end
tv.peptide_allele_string tv.consequence_type
);
}
1;
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