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Summary

Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor

Package variables

Included modules

Inherit

Bio::EnsEMBL::DBSQL::BaseAdaptor

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";
  }

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.

Methods

Methods description

    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

  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

Methods code

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;

}

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 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;

}

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.
#

}

General documentation

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