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Summary

Bio::EnsEMBL::Variation::DBSQL::IndividualGenotypeAdaptor

Package variables

Included modules

Inherit

Bio::EnsEMBL::Variation::DBSQL::BaseGenotypeAdaptor

Synopsis

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

  $iga = $db->get_IndividualGenotypeAdaptor();
  $ia  = $db->get_IndividualAdaptor();

  # Get an IndividualGenotype by its internal identifier
  $igtype = $ia->fetch_by_dbID(145);

  # Get all individual genotypes for an individual
  $ind = $ia->fetch_all_by_Individual(1219);

  foreach $igtype (@{$iga->fetch_all_by_Individual($ind)}) {
    print $igtype->variation()->name(),  ' ',
          $igtype->allele1(), '/', $igtype->allele2(), "\n";
  }

Description

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

Methods

Methods description

  Arg [1]    : Bio::EnsEMBL::Variation::Individual
  Example    : $ind = $ind_adaptor->fetch_by_dbID(1345);
               @gtys = $igty_adaptor->fetch_all_by_Individual($ind);
  Description: Retrieves all genotypes which are stored for a specified
               individual.
  Returntype : Bio::EnsEMBL::Variation::IndividualGenotype
  Exceptions : throw on incorrect argument
  Caller     : general
  Status     : At Risk

  Arg [1]    : Bio::EnsEMBL::Variation $variation
  Example    : my $var = $variation_adaptor->fetch_by_name( "rs1121" )
               $igtypes = $igtype_adaptor->fetch_all_by_Variation( $var )
  Description: Retrieves a list of individual genotypes for the given Variation.
               If none are available an empty listref is returned.
  Returntype : listref Bio::EnsEMBL::Variation::IndividualGenotype 
  Exceptions : none
  Caller     : general
  Status     : At Risk

Methods code

sub fetch_all_by_Individual {

  my $self = shift;
  my $ind = shift;
  

  $self->_multiple(0); #to return data from single and multiple genotype table
  return $self->SUPER::fetch_all_by_Individual($ind);

}

sub fetch_all_by_Slice {

    my $self = shift;
    my $slice = shift;
    
    $self->_multiple(0);
    my @final_genotypes;
    push @final_genotypes, @{$self->SUPER::fetch_all_by_Slice($slice)};
    $self->_multiple(1);
    $self->SUPER::fetch_all_by_Slice($slice);
    push @final_genotypes, @{$self->SUPER::fetch_all_by_Slice($slice)};
    return\@ final_genotypes;
}

1;

}

sub fetch_all_by_Variation {

    my $self = shift;
    my $variation = shift;
    $self->_multiple(0); #to return data from single and multiple table
    return $self->SUPER::fetch_all_by_Variation($variation);

}

General documentation

Post questions to the Ensembl development list ensembl-dev@ebi.ac.uk