Toolbar

Summary

Bio::EnsEMBL::Variation::DBSQL::PopulationAdaptor

Package variables

Included modules

Inherit

Bio::EnsEMBL::Variation::DBSQL::SampleAdaptor

Synopsis

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

  $pa = $db->get_PopulationAdaptor();

  # Get a Population by its internal identifier
  $pop = $pa->fetch_by_dbID(145);

  # fetch a population by its name
  $pop = $pa->fetch_by_name('PACIFIC'); 

  # fetch all sub populations of a population
  foreach $sub_pop (@{$pa->fetch_all_by_super_Population($pop)}) {
    print $sub_pop->name(), " is a sub population of ", $pop->name(), "\n";
  }

  # fetch all super populations
  foreach $super_pop (@{$pa->fetch_all_by_sub_Population($pop)}) {
    print $pop->name(), " is a sub population of ", $super_pop->name(), "\n";
  }

Description

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

Methods

Methods description

  Arg [1]     : Bio::EnsEMBL::Variation::Individual $ind
  Example     : my $ind = $ind_adaptor->fetch_by_name('NA12004');
                foreach my $pop (@{$pop_adaptor->fetch_all_by_Individual($ind)}){
		    print $pop->name,"\n";
                }
  Description : Retrieves all populations from a specified individual
  ReturnType  : reference to list of Bio::EnsEMBL::Variation::Population objects
  Exceptions  : throw if incorrect argument is passed
                warning if provided individual does not have a dbID
  Caller      : general
  Status      : At Risk

  Arg [1]    : Bio::EnsEMBL::Variation::Population $pop
  Example    : foreach $super_pop (@{$pa->fetch_all_by_sub_Population($pop)}) {
                 print $super_pop->name(), "\n";
               }
  Description: Retrieves all super populations for a provided population
  Returntype : Bio::EnsEMBL::Population
  Exceptions : throw on bad argument
  Caller     : general
  Status     : At Risk

  Arg [1]    : Bio::EnsEMBL::Variation::Population $pop
  Example    : foreach $sub_pop (@{$pa->fetch_all_by_super_Population($pop)}) {
                 print $sub_pop->name(), "\n";
               }
  Description: Retrieves all sub populations of a provided population.
  Returntype : Bio::EnsEMBL::Population
  Exceptions : throw on bad argument
  Caller     : general
  Status     : At Risk

  Arg [1]    : string $name
  Example    : $pop = $pop_adaptor->fetch_by_name('NUSPAE:Singapore_HDL');
  Description: Retrieves a population object via its name
  Returntype : Bio::EnsEMBL::Variation::Population
  Exceptions : throw if name argument is not defined
  Caller     : general
  Status     : At Risk

    Args        : none
    Example     : $population = $pop_adaptor->fetch_default_LDPopulation();
    Description : Obtains the population it is used as a default in the LD display of the pairwise LD data
    ReturnType  : Bio::EnsEMBL::Variation::Population
    Exceptions  : none
    Caller      : general
    Status      : At Risk

    Arg [1]              : $population_synonym
    Example              : my $pop = $pop_adaptor->fetch_population_by_synonym($population_synonym,$source);
    Description          : Retrieves populations for the synonym given in the source. If no source is provided, retrieves all the synonyms
    Returntype           : list of Bio::EnsEMBL::Variation::Population
    Exceptions           : none
    Caller               : general
    Status               : At Risk

  Arg [1]     : Bio::EnsEMBL::Variation::VariationFeature $vf
  Example     : my $vf = $vf_adaptor->fetch_by_name('rs205621');
                my $populations_tagged = $vf->is_tagged();
                foreach my $pop (@{$vf_adaptor->is_tagged}){
		    print $pop->name," has been tagged using a 0.99 r2 criteria\n";
                }
  Description : Retrieves all populations from a specified variation feature that have been tagged
  ReturnType  : reference to list of Bio::EnsEMBL::Variation::Population objects
  Exceptions  : throw if incorrect argument is passed
                warning if provided variation feature does not have a dbID
  Caller      : general
  Status      : At Risk

Methods code

sub _columns {

    return qw(s.sample_id s.name s.size s.description);

}

sub _default_where_clause {

    return 's.sample_id = p.sample_id';
}

1;

}

sub _objs_from_sth {

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

  my @pops;

  my ($pop_id, $name, $size, $desc);

  $sth->bind_columns(\$pop_id,\$ name,\$ size,\$ desc);

  while($sth->fetch()) {
    push @pops, Bio::EnsEMBL::Variation::Population->new
      (-dbID => $pop_id,
       -ADAPTOR => $self,
       -NAME => $name,
       -DESCRIPTION => $desc,
       -SIZE => $size);
  }

  return\@ pops;

}

sub _tables{return {

(['population','p'],		    ['sample','s']);

}

sub fetch_all_by_Individual {

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

    if(!ref($ind) || !$ind->isa('Bio::EnsEMBL::Variation::Individual')) {
	throw("Bio::EnsEMBL::Variation::Individual arg expected");
    }
    
    if(!$ind->dbID()) {
	warning("Individual does not have dbID, cannot retrieve Individuals");
	return [];
  } 

    my $sth = $self->prepare(qq{SELECT p.sample_id, s.name, s.size, s.description
				FROM population p, individual_population ip, sample s
				WHERE s.sample_id = ip.population_sample_id
				AND s.sample_id = p.sample_id
                                AND ip.individual_sample_id = ?
			    });
    $sth->bind_param(1,$ind->dbID,SQL_INTEGER);
    $sth->execute();

    my $results = $self->_objs_from_sth($sth);

    $sth->finish();

    return $results;

}

sub fetch_all_by_sub_Population {

  my $self = shift;
  my $pop  = shift;

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

  if(!$pop->dbID()) {
    warning("Cannot retrieve super populations for population without dbID");
    return [];
  }

  my $sth = $self->prepare(q{SELECT p.sample_id, s.name, s.size,
                                    s.description
                             FROM   population p, population_structure ps, sample s
                             WHERE  p.sample_id = ps.super_population_sample_id
                             AND    ps.sub_population_sample_id = ?
			     AND    p.sample_id = s.sample_id});

  $sth->bind_param(1,$pop->dbID,SQL_INTEGER);
  $sth->execute();

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

  $sth->finish();

  return $result;

}

sub fetch_all_by_super_Population {

  my $self = shift;
  my $pop  = shift;

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

  if(!$pop->dbID()) {
    warning("Cannot retrieve sub populations for population without dbID");
    return [];
  }

  my $sth = $self->prepare(q{SELECT p.sample_id, s.name, s.size,
                                    s.description
                             FROM   population p, population_structure ps, sample s
                             WHERE  p.sample_id = ps.sub_population_sample_id
                             AND    ps.super_population_sample_id = ?
			     AND    p.sample_id = s.sample_id});

  $sth->bind_param(1,$pop->dbID,SQL_INTEGER);
  $sth->execute();

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

  $sth->finish();

  return $result;

}

sub fetch_by_name {

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

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

  my $sth = $self->prepare(q{SELECT p.sample_id, s.name, s.size, s.description
                             FROM   population p, sample s
                             WHERE  s.name = ?
			     AND    s.sample_id = p.sample_id});

  $sth->bind_param(1,$name,SQL_VARCHAR);
  $sth->execute();

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

  $sth->finish();

  return undef if(!@$result);

  return $result->[0];

}

sub fetch_default_LDPopulation {

    my $self = shift;
    my $population_id;
    
    my $sth = $self->prepare(qq{SELECT meta_value from meta where meta_key = ?});

    $sth->bind_param(1,'pairwise_ld.default_population',SQL_VARCHAR);
    $sth->execute();
    $sth->bind_columns(\$population_id);
    $sth->fetch();
    $sth->finish;

    if (defined $population_id){
	return $self->fetch_by_dbID($population_id);
    }
    else{
	return undef;
    }

}

sub fetch_population_by_synonym {

    my $self = shift;
    my $synonym_name = shift;
    my $source = shift;
    my $pops;
    my $pop;
    #return all sample_id from the database
    my $samples = $self->SUPER::fetch_sample_by_synonym($synonym_name, $source);
    foreach my $sample_id (@{$samples}){
	#get the ones that are individuals
	$pop = $self->fetch_by_dbID($sample_id);
	push @{$pops}, $pop if (defined $pop);
    }
    return $pops;

}

sub fetch_tagged_Population {

    my $self = shift;
    my $variation_feature = shift;

    if(!ref($variation_feature) || !$variation_feature->isa('Bio::EnsEMBL::Variation::VariationFeature')) {
	throw("Bio::EnsEMBL::Variation::VariationFeature arg expected");
    }
    
    if(!$variation_feature->dbID()) {
	warning("Variation feature does not have dbID, cannot retrieve tagged populations");
	return [];
  } 

    my $sth = $self->prepare(qq{SELECT p.sample_id, s.name, s.size, s.description
				FROM population p, tagged_variation_feature tvf, sample s
				WHERE p.sample_id = tvf.sample_id
				AND   s.sample_id = p.sample_id
                                AND   tvf.variation_feature_id = ?
			    });
    $sth->bind_param(1,$variation_feature->dbID,SQL_INTEGER);
    $sth->execute();
    my $results = $self->_objs_from_sth($sth);

    $sth->finish();

    return $results;
}

#
# private method, creates population objects from an executed statement handle
# ordering of columns must be consistant
#

}

General documentation

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