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Summary

Bio::EnsEMBL::Variation::DBSQL::VariationGroupAdaptor

Package variables

Included modules

Inherit

Bio::EnsEMBL::DBSQL::BaseAdaptor

Synopsis

  $db = Bio::EnsEMBL::Variation::DBSQL::DBAdaptor->new(...);

  $vga = $db->get_VariationGroupAdaptor();

  # retrieve a variation group by its name
  $vg = $vga->fetch_by_name('PERLEGEN:B000009');

  # retrieve a variation group by its internal identifier
  $vg = $vga->fetch_by_dbID(63211);

  # retrieve all variation groups which a variation is a part of
  @vgs = @{$vga->fetch_all_by_Variation($var)};

Description

This adaptor provides database connectivity for VariationGroup objects.
VariationGroups may be retrieved from the Ensembl variation database by
several means using this module.

Methods

Methods description

  Arg [1]    : Bio::EnsEMBL::Variation::Variation
  Example    : my $vgs = $vga->fetch_all_by_Variation($var);
  Description: Retrieves all variation groups which a particular variation
               is present in.
  Returntype : reference to list of Bio::EnsEMBL::Variation::VariationGroups
  Exceptions : throw on incorrect argument
  Caller     : general
  Status     : At Risk

  Arg [1]    : int $dbID
  Example    : $vg = $vg_adaptor->fetch_by_dbID(5526);
  Description: Retrieves a VariationGroup object via its internal identifier.
               If no such variation group exists undef is returned.
  Returntype : Bio::EnsEMBL::Variation::VariationGroup
  Exceptions : throw if dbID arg is not defined
  Caller     : general
  Status     : At Risk

  Arg [1]    : string $name
  Example    : $vg = $vga->fetch_by_name('PERLEGEN:B000009');
  Description: Retrieves a variation group by its name
  Returntype : Bio::EnsEMBL::Variation::VariationGroup
  Exceptions : throw if name argument is not provided
  Caller     : general
  Status     : At Risk

Methods code

sub _objs_from_sth {

  my $self = shift;
  my $sth  = shift;

  my ($vg_id, $name, $source, $type, $var_id);
  $sth->bind_columns(\$vg_id,\$ name,\$ source,\$ type,\$ var_id);

  my %seen_vars;

  my @results;

  my ($cur_vg, $cur_vg_id);

  # construct all variation groups without their associated variations

  while($sth->fetch()) {
    if(!defined($cur_vg) || $cur_vg_id != $vg_id) {
      $cur_vg = Bio::EnsEMBL::Variation::VariationGroup->new
        (-dbID => $vg_id,
         -adaptor => $self,
         -name    => $name,
         -type    => $type,
         -source  => $source);
      $cur_vg_id = $vg_id;
      push @results, $cur_vg;
    }

    if(defined($var_id)) {
      $seen_vars{$var_id} ||= [];
      push @{$seen_vars{$var_id}}, $cur_vg;
    }
  }

  # fetch all of the variations at once and add them to the variation groups

  my @var_ids = keys %seen_vars;
  my $va = $self->db->get_VariationAdaptor();
  my $vars = $va->fetch_all_by_dbID_list(\@var_ids);

  foreach my $var (@$vars) {
    foreach my $vg (@{$seen_vars{$var->dbID()}}) {
      $vg->add_Variation($var);
    }
  }

  return\@ results;
}




1;

}

sub fetch_all_by_Variation {

  my $self = shift;
  my $var  = shift;

  if(!ref($var) || !$var->isa('Bio::EnsEMBL::Variation::Variation')) {
    throw('Bio::EnsEMBL::Variation::Variation argument expected');
  }

  my $sth = $self->prepare
    (q{SELECT vg.variation_group_id, vg.name, s.name, vg.type, vgv.variation_id
       FROM   variation_group vg, source s, variation_group_variation vgv
       WHERE  vg.source_id = s.source_id
       AND    vgv.variation_group_id = vg.variation_group_id
       AND    vgv.variation_id = ?
       ORDER BY vg.variation_group_id});
  $sth->bind_param(1,$var->dbID,SQL_INTEGER);
  $sth->execute();

  my $result = $self->_objs_from_sth($sth);
  $sth->finish();

  return $result;

}

sub fetch_by_dbID {

  my $self = shift;
  my $dbID = shift;

  throw('dbID argument expected') if(!defined($dbID));

  # left join allows variation groups without any variations to be fetched

  my $sth = $self->prepare
    (q{SELECT vg.variation_group_id, vg.name, s.name, vg.type, vgv.variation_id
       FROM   (variation_group vg, source s)
       LEFT JOIN variation_group_variation vgv ON
                 vgv.variation_group_id = vg.variation_group_id
       WHERE  vg.source_id = s.source_id
       AND    vg.variation_group_id = ?});
  $sth->bind_param(1,$dbID,SQL_INTEGER);
  $sth->execute();

  my $result = $self->_objs_from_sth($sth);
  $sth->finish();

  return undef if(!@$result);

  return $result->[0];

}

sub fetch_by_name {

  my $self = shift;
  my $name = shift;

  throw('name argument expected') if(!defined($name));

  # left join allows variation groups without any variations to be fetched

  my $sth = $self->prepare
    (q{SELECT vg.variation_group_id, vg.name, s.name, vg.type, vgv.variation_id
       FROM   (variation_group vg, source s)
       LEFT JOIN variation_group_variation vgv
       ON    vgv.variation_group_id = vg.variation_group_id
       WHERE  vg.source_id = s.source_id
       AND    vg.name = ?});
  $sth->bind_param(1,$name,SQL_VARCHAR);
  $sth->execute();

  my $result = $self->_objs_from_sth($sth);
  $sth->finish();

  return undef if(!@$result);

  return $result->[0];

}

General documentation

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