comparison variant_effect_predictor/Bio/EnsEMBL/DBSQL/OntologyTermAdaptor.pm @ 0:1f6dce3d34e0

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=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::DBSQL::OntologyTermAdaptor

=head1 SYNOPSIS

  my $goa =
    $registry->get_adaptor( 'Multi', 'Ontology', 'OntologyTerm' );

  my $term = $goa->fetch_by_accession('GO:0010885');

  my @children    = @{ $goa->fetch_all_by_parent_term($term) };
  my @descendants = @{ $goa->fetch_all_by_ancestor_term($term) };

  my @parents   = @{ $goa->fetch_all_by_child_term($term) };
  my @ancestors = @{ $goa->fetch_all_by_descendant_term($term) };

  my %ancestor_chart = %{ $goa->_fetch_ancestor_chart($term) };

=head1 DESCRIPTION

An abstract adaptor class for fetching ontology
terms, creates Bio::EnsEMBL::OntologyTerm objects.

=head1 METHODS

=cut

package Bio::EnsEMBL::DBSQL::OntologyTermAdaptor;

use strict;
use warnings;

use DBI qw( :sql_types );

use Bio::EnsEMBL::Utils::Exception qw( throw );
use Bio::EnsEMBL::Utils::Scalar qw( assert_ref );

use Bio::EnsEMBL::OntologyTerm;

use base qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );

=head2 fetch_all_by_name

  Arg [1]       : String, name of term, or SQL pattern
  Arg [2]       : (optional) String, name of ontology

  Description   : Fetches ontology term(s) given a name, a synonym, or a
                  SQL pattern like "%splice_site%"

  Example       :

    my ($term) =
      @{ $ot_adaptor->fetch_by_name( 'DNA_binding_site', 'SO' ) };

    # Will find terms in both SO and GO:
    my @terms = @{ $ot_adaptor->fetch_by_name('%splice_site%') };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

=cut

sub fetch_all_by_name {
  my ( $this, $pattern, $ontology ) = @_;

  my $statement = q(
SELECT DISTINCT
        term.term_id,
        term.accession,
        term.name,
        term.definition,
        term.subsets,
        ontology.namespace
FROM    ontology
  JOIN  term USING (ontology_id)
  LEFT JOIN  synonym USING (term_id)
WHERE   ( term.name LIKE ? OR synonym.name LIKE ? ));

  if ( defined($ontology) ) {
    $statement .= " AND ontology.name = ?";
  }

  my $sth = $this->prepare($statement);
  $sth->bind_param( 1, $pattern, SQL_VARCHAR );
  $sth->bind_param( 2, $pattern, SQL_VARCHAR );

  if ( defined($ontology) ) {
    $sth->bind_param( 3, $ontology, SQL_VARCHAR );
  }

  $sth->execute();

  my ( $dbid, $accession, $name, $definition, $subsets, $namespace );
  $sth->bind_columns(
     \( $dbid, $accession, $name, $definition, $subsets, $namespace ) );

  my @terms;

  while ( $sth->fetch() ) {
    $subsets ||= '';

    push @terms,
      Bio::EnsEMBL::OntologyTerm->new(
                               '-dbid'      => $dbid,
                               '-adaptor'   => $this,
                               '-accession' => $accession,
                               '-namespace' => $namespace,
                               '-subsets' => [ split( /,/, $subsets ) ],
                               '-name'    => $name,
                               '-definition' => $definition, );
  }

  return \@terms;
} ## end sub fetch_all_by_name


=head2 fetch_by_accession

  Arg [1]       : String

  Description   : Fetches an ontology term given an accession.

  Example       :

    my $term = $ot_adaptor->fetch_by_accession('GO:0030326');

  Return type   : Bio::EnsEMBL::OntologyTerm

=cut

sub fetch_by_accession {
  my ( $this, $accession ) = @_;

  my $statement = q(
SELECT  term.term_id,
        term.name,
        term.definition,
        term.subsets,
        ontology.name,
        ontology.namespace
FROM    ontology
  JOIN  term USING (ontology_id)
WHERE   term.accession = ?);

  my $sth = $this->prepare($statement);
  $sth->bind_param( 1, $accession, SQL_VARCHAR );

  $sth->execute();

  my ( $dbid, $name, $definition, $subsets, $ontology, $namespace );
  $sth->bind_columns(
      \( $dbid, $name, $definition, $subsets, $ontology, $namespace ) );

  $sth->fetch();
  $subsets ||= '';

  my $term =
    Bio::EnsEMBL::OntologyTerm->new(
                    '-dbid'       => $dbid,
                    '-adaptor'    => $this,
                    '-accession'  => $accession,
                    '-ontology'   => $ontology,
                    '-namespace'  => $namespace,
                    '-subsets'    => [ split( /,/, $subsets ) ],
                    '-name'       => $name,
                    '-definition' => $definition,
                    '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
    );
  $sth->finish();

  return $term;
} ## end sub fetch_by_accession

=head2 fetch_all_by_parent_term

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose children terms should be fetched.

  Description   : Given a parent ontology term, returns a list of
                  its immediate children terms.

  Example       :

    my @children =
      @{ $ot_adaptor->fetch_all_by_parent_term($term) };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

=cut

sub fetch_all_by_parent_term {
  my ( $this, $term ) = @_;

  assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );

  my @terms;

  if ( !$term->{'child_terms_fetched'} ) {
    my $statement = q(
SELECT  child_term.term_id,
        child_term.accession,
        child_term.name,
        child_term.definition,
        child_term.subsets,
        rt.name
FROM    term child_term
  JOIN  relation ON (relation.child_term_id = child_term.term_id)
  JOIN  relation_type rt USING (relation_type_id)
WHERE   relation.parent_term_id = ?);

    my $sth = $this->prepare($statement);
    $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );

    $sth->execute();

    my ( $dbid, $accession, $name, $definition, $subsets, $relation );
    $sth->bind_columns(
      \( $dbid, $accession, $name, $definition, $subsets, $relation ) );

    while ( $sth->fetch() ) {
      $subsets ||= '';

      my $child_term =
        Bio::EnsEMBL::OntologyTerm->new(
                               '-dbid'      => $dbid,
                               '-adaptor'   => $this,
                               '-accession' => $accession,
                               '-ontology'  => $term->{'ontology'},
                               '-namespace' => $term->{'namespace'},
                               '-subsets' => [ split( /,/, $subsets ) ],
                               '-name'    => $name,
                               '-definition' => $definition, );

      push( @terms,                              $child_term );
      push( @{ $term->{'children'}{$relation} }, $child_term );
    }

    $term->{'child_terms_fetched'} = 1;
  } else {
    foreach my $relation ( values( %{ $term->{'children'} } ) ) {
      push( @terms, @{$relation} );
    }
  }

  return \@terms;
} ## end sub fetch_all_by_parent_term

=head2 fetch_all_by_ancestor_term

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose descendant terms should be fetched.

  Description   : Given a parent ontology term, returns a list of
                  all its descendant terms, down to and including
                  any leaf terms.  Relations of the type 'is_a' and
                  'part_of' are followed.

  Example       :

    my @descendants =
      @{ $ot_adaptor->fetch_all_by_ancestor_term($term) };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

=cut

sub fetch_all_by_ancestor_term {
  my ( $this, $term ) = @_;

  assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );

  my $statement = q(
SELECT DISTINCT
        child_term.term_id,
        child_term.accession,
        child_term.name,
        child_term.definition,
        child_term.subsets
FROM    term child_term
  JOIN  closure ON (closure.child_term_id = child_term.term_id)
WHERE   closure.parent_term_id = ?
  AND   closure.distance > 0
ORDER BY closure.distance, child_term.accession);

  my $sth = $this->prepare($statement);
  $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );

  $sth->execute();

  my ( $dbid, $accession, $name, $definition, $subsets );
  $sth->bind_columns(
                 \( $dbid, $accession, $name, $definition, $subsets ) );

  my @terms;

  while ( $sth->fetch() ) {
    $subsets ||= '';

    push( @terms,
          Bio::EnsEMBL::OntologyTerm->new(
                               '-dbid'      => $dbid,
                               '-adaptor'   => $this,
                               '-accession' => $accession,
                               '-ontology'  => $term->{'ontology'},
                               '-namespace' => $term->{'namespace'},
                               '-subsets' => [ split( /,/, $subsets ) ],
                               '-name'    => $name,
                               '-definition' => $definition, ) );
  }

  return \@terms;
} ## end sub fetch_all_by_ancestor_term

=head2 fetch_all_by_child_term

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose parent terms should be fetched.

  Description   : Given a child ontology term, returns a list of
                  its immediate parent terms.

  Example       :

    my @parents = @{ $ot_adaptor->fetch_all_by_child_term($term) };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

=cut

sub fetch_all_by_child_term {
  my ( $this, $term ) = @_;

  assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );

  my @terms;

  if ( !$term->{'parent_terms_fetched'} ) {
    my $statement = q(
SELECT  parent_term.term_id,
        parent_term.accession,
        parent_term.name,
        parent_term.definition,
        parent_term.subsets,
        rt.name
FROM    term parent_term
  JOIN  relation ON (relation.parent_term_id = parent_term.term_id)
  JOIN  relation_type rt USING (relation_type_id)
WHERE   relation.child_term_id = ?);

    my $sth = $this->prepare($statement);
    $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );

    $sth->execute();

    my ( $dbid, $accession, $name, $definition, $subsets, $relation );
    $sth->bind_columns(
      \( $dbid, $accession, $name, $definition, $subsets, $relation ) );

    while ( $sth->fetch() ) {
      $subsets ||= '';

      my $parent_term =
        Bio::EnsEMBL::OntologyTerm->new(
                               '-dbid'      => $dbid,
                               '-adaptor'   => $this,
                               '-accession' => $accession,
                               '-ontology'  => $term->{'ontology'},
                               '-namespace' => $term->{'namespace'},
                               '-subsets' => [ split( /,/, $subsets ) ],
                               '-name'    => $name,
                               '-definition' => $definition, );

      push( @terms,                             $parent_term );
      push( @{ $term->{'parents'}{$relation} }, $parent_term );
    }

    $term->{'parent_terms_fetched'} = 1;
  } else {
    foreach my $relation ( values( %{ $term->{'parents'} } ) ) {
      push( @terms, @{$relation} );
    }
  }

  return \@terms;
} ## end sub fetch_all_by_child_term

=head2 fetch_all_by_descendant_term

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose ancestor terms should be fetched.

  Arg [2]       : (optional) String
                  The subset within the ontolgy to which the query
                  should be restricted.  The subset may be specified as
                  a SQL pattern, e.g., "%goslim%" (but "goslim%" might
                  not do what you expect), or as a specific subset name,
                  e.g., "goslim_generic".

  Arg [3]       : (optional) Boolean
                  If true (non-zero), only return the closest
                  term(s).  If this argument is true, and the
                  previous argument is left undefined, this method
                  will return the parent(s) of the given term.
  
  Arg [4]       : (optional) Boolean
                  If true we will allow the retrieval of terms whose distance
                  to the current term is 0. If false then we will only return
                  those which are above the current term in the ontology

  Description   : Given a child ontology term, returns a list of
                  all its ancestor terms, up to and including any
                  root term.  Relations of the type 'is_a' and
                  'part_of' are followed.  Optionally, only terms in
                  a given subset of the ontology may be returned,
                  and additionally one may ask to only get the
                  closest term(s) to the given child term.

  Example       :

    my @ancestors =
      @{ $ot_adaptor->fetch_all_by_descendant_term($term) };

  Return type   : listref of Bio::EnsEMBL::OntologyTerm

=cut

sub fetch_all_by_descendant_term {
  my ( $this, $term, $subset, $closest_only, $allow_zero_distance ) = @_;

  assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );

  $closest_only ||= 0;

  my $statement = q(
SELECT DISTINCT
        parent_term.term_id,
        parent_term.accession,
        parent_term.name,
        parent_term.definition,
        parent_term.subsets,
        closure.distance
FROM    term parent_term
  JOIN  closure ON (closure.parent_term_id = parent_term.term_id)
WHERE   closure.child_term_id = ?
  AND   closure.distance > ?);

  if ( defined($subset) ) {
    if ( index( $subset, '%' ) != -1 ) {
      $statement .= q(
  AND   parent_term.subsets LIKE ?);
    } else {
      $statement .= q(
  AND   FIND_IN_SET(?, parent_term.subsets) > 0);
    }
  }

  $statement .= q(
ORDER BY closure.distance, parent_term.accession);

  my $sth = $this->prepare($statement);
  $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );
  my $query_distance = ($allow_zero_distance) ? -1 : 0;
  $sth->bind_param( 2, $query_distance, SQL_INTEGER );

  if ( defined($subset) ) {
    $sth->bind_param( 3, $subset, SQL_VARCHAR );
  }

  $sth->execute();

  my ( $dbid, $accession, $name, $definition, $subsets, $distance );
  $sth->bind_columns(
      \( $dbid, $accession, $name, $definition, $subsets, $distance ) );

  my @terms;
  my $min_distance;

  while ( $sth->fetch() ) {
    $subsets ||= '';
    $min_distance ||= $distance;

    if ( !$closest_only || $distance == $min_distance ) {
      push( @terms,
            Bio::EnsEMBL::OntologyTerm->new(
                               '-dbid'      => $dbid,
                               '-adaptor'   => $this,
                               '-accession' => $accession,
                               '-ontology'  => $term->{'ontology'},
                               '-namespace' => $term->{'namespace'},
                               '-subsets' => [ split( /,/, $subsets ) ],
                               '-name'    => $name,
                               '-definition' => $definition, ) );
    } else {
      $sth->finish();
      last;
    }
  }

  return \@terms;
} ## end sub fetch_all_by_descendant_term

sub _fetch_synonyms_by_dbID {
  my ( $this, $dbID ) = @_;

  my $statement = q(
SELECT  synonym.name
FROM    synonym
WHERE   synonym.term_id = ?);

  my $sth = $this->prepare($statement);
  $sth->bind_param( 1, $dbID, SQL_INTEGER );

  $sth->execute();

  my $synonym;
  $sth->bind_col( 1, \$synonym );

  my @synonyms;
  while ( $sth->fetch() ) {
    push( @synonyms, $synonym );
  }

  return \@synonyms;
}



=head2 _fetch_ancestor_chart

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose ancestor terms should be fetched.

  Description   : Given a child ontology term, returns a hash
                  structure containing its ancestor terms, up to and
                  including any root term.  Relations of the type
                  'is_a' and 'part_of' are included.

  Example       :

    my %chart = %{ $ot_adaptor->_fetch_ancestor_chart($term) };

  Return type   : A reference to a hash structure like this:

    {
      'GO:XXXXXXX' => {
        'term' =>           # ref to Bio::EnsEMBL::OntologyTerm object
        'is_a'    => [...], # listref of Bio::EnsEMBL::OntologyTerm
        'part_of' => [...], # listref of Bio::EnsEMBL::OntologyTerm
      },
      'GO:YYYYYYY' => {
        # Similarly for all ancestors,
        # and including the query term itself.
      }
    }

=cut

sub _fetch_ancestor_chart {
  my ( $this, $term ) = @_;

  assert_ref( $term, 'Bio::EnsEMBL::OntologyTerm' );

  my $statement = q(
SELECT  subparent_term.term_id,
        parent_term.term_id,
        relation_type.name
FROM    closure
  JOIN  relation
    ON (relation.parent_term_id = closure.parent_term_id
      AND relation.child_term_id = closure.subparent_term_id)
  JOIN  relation_type USING (relation_type_id)
  JOIN  term subparent_term
    ON (subparent_term.term_id = closure.subparent_term_id)
  JOIN  term parent_term ON (parent_term.term_id = closure.parent_term_id)
WHERE   closure.child_term_id = ?
ORDER BY closure.distance);

  my $sth = $this->prepare($statement);
  $sth->bind_param( 1, $term->dbID(), SQL_INTEGER );

  $sth->execute();

  my ( $subparent_id, $parent_id, $relation );
  $sth->bind_columns( \( $subparent_id, $parent_id, $relation ) );

  my %id_chart;
  my %acc_chart;

  while ( $sth->fetch() ) {
    if ( !exists( $id_chart{$parent_id} ) ) {
      $id_chart{$parent_id} = {};
    }
    push( @{ $id_chart{$subparent_id}{$relation} }, $parent_id );
  }

  my @terms = @{ $this->fetch_all_by_dbID_list( [ keys(%id_chart) ] ) };

  foreach my $term (@terms) {
    $id_chart{ $term->dbID() }{'term'}       = $term;
    $acc_chart{ $term->accession() }{'term'} = $term;
  }

  foreach my $term (@terms) {
    my $accession = $term->accession();
    my $dbID      = $term->dbID();

    foreach my $relation ( keys( %{ $id_chart{$dbID} } ) ) {
      if ( $relation eq 'term' ) { next }

      foreach my $id ( @{ $id_chart{$dbID}{$relation} } ) {
        push( @{ $acc_chart{$accession}{$relation} },
              $id_chart{$id}{'term'} );
      }
    }
  }

  return \%acc_chart;
} ## end sub _fetch_ancestor_chart

#-----------------------------------------------------------------------
# Useful public methods that implement functionality not properly
# provided by the parent class Bio::EnsEMBL::DBSQL::BaseAdaptor.

sub fetch_by_dbID {
  my ( $this, $dbid ) = @_;

  my $statement = q(
SELECT  term.accession,
        term.name,
        term.definition,
        term.subsets,
        ontology.name,
        ontology.namespace
FROM    ontology
  JOIN  term USING (ontology_id)
WHERE   term.term_id = ?);

  my $sth = $this->prepare($statement);
  $sth->bind_param( 1, $dbid, SQL_INTEGER );

  $sth->execute();

  my ( $accession, $name, $definition, $subsets, $ontology,
       $namespace );
  $sth->bind_columns(
      \( $accession, $name, $definition, $subsets, $ontology, $namespace
      ) );

  $sth->fetch();
  $subsets ||= '';

  my $term =
    Bio::EnsEMBL::OntologyTerm->new(
                    '-dbid'       => $dbid,
                    '-adaptor'    => $this,
                    '-accession'  => $accession,
                    '-ontology'   => $ontology,
                    '-namespace'  => $namespace,
                    '-subsets'    => [ split( /,/, $subsets ) ],
                    '-name'       => $name,
                    '-definition' => $definition,
                    '-synonyms' => $this->_fetch_synonyms_by_dbID($dbid)
    );
  $sth->finish();

  return $term;
} ## end sub fetch_by_dbID

sub fetch_all_by_dbID_list {
  my ( $this, $dbids ) = @_;

  if ( !@{$dbids} ) { return [] }

  my $stmt = q(
SELECT  term.term_id,
        term.accession,
        term.name,
        term.definition,
        term.subsets,
        ontology.name,
        ontology.namespace
FROM    ontology
  JOIN  term USING (ontology_id)
WHERE   term.term_id IN (%s));

  my $statement = sprintf(
    $stmt,
    join(
      ',',
      map {
        $this->dbc()->db_handle()->quote( $_, SQL_INTEGER )
        } @{$dbids} ) );

  my $sth = $this->prepare($statement);

  $sth->execute();

  my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
       $namespace );
  $sth->bind_columns( \( $dbid,    $accession, $name, $definition,
                         $subsets, $ontology,  $namespace ) );

  my @terms;

  while ( $sth->fetch() ) {
    $subsets ||= '';

    push( @terms,
          Bio::EnsEMBL::OntologyTerm->new(
                               '-dbid'      => $dbid,
                               '-adaptor'   => $this,
                               '-accession' => $accession,
                               '-ontology'  => $ontology,
                               '-namespace' => $namespace,
                               '-subsets' => [ split( /,/, $subsets ) ],
                               '-name'    => $name,
                               '-definition' => $definition, ) );
  }

  return \@terms;
} ## end sub fetch_all_by_dbID_list

sub fetch_all {
  my ($this) = @_;

  my $statement = q(
SELECT  term.term_id,
        term.accession,
        term.name,
        term.definition,
        term.subsets,
        ontology.name,
        ontology.namespace
FROM    ontology
  JOIN  term USING (ontology_id));

  my $sth = $this->prepare($statement);
  $sth->execute();

  my ( $dbid, $accession, $name, $definition, $subsets, $ontology,
       $namespace );
  $sth->bind_columns( \( $dbid,    $accession, $name, $definition,
                         $subsets, $ontology,  $namespace ) );

  my @terms;

  while ( $sth->fetch() ) {
    $subsets ||= '';

    push( @terms,
          Bio::EnsEMBL::OntologyTerm->new(
                               '-dbid'      => $dbid,
                               '-adaptor'   => $this,
                               '-accession' => $accession,
                               '-ontology'  => $ontology,
                               '-namespace' => $namespace,
                               '-subsets' => [ split( /,/, $subsets ) ],
                               '-name'    => $name,
                               '-definition' => $definition ) );
  }

  return \@terms;
} ## end sub fetch_all

1;