view variant_effect_predictor/Bio/EnsEMBL/DBSQL/RepeatConsensusAdaptor.pm @ 0:1f6dce3d34e0

Uploaded

=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::RepeatConsensusAdaptor

=head1 SYNOPSIS

  $rca = $database_adaptor->get_RepeatConsensusAdaptor();

  $repeat_consensus = $rca->fetch_by_dbID(132);
  $repeat_consensus = $rca->fetch_by_name_class( 'AluSx', 'SINE/Alu' );

  $rca->store( $rc1, $rc2, $rc3 );

=head1 DESCRIPTION

This is an adaptor for the retrieval and storage of RepeatConsensus
objects.

=head1 METHODS

=cut

package Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor;

use strict;
use warnings;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::RepeatConsensus;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate);

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

=head2 fetch_all_repeat_types

  Example			: my $types = $rca->fetch_all_repeat_types();
  Description	: Returns the distinct repeat types available from a database
  Returntype 	: Array
  Exceptions 	: -

=cut


sub fetch_all_repeat_types {
  my ($self) = @_;
  return $self->dbc()->sql_helper()->execute_simple(
    -SQL => 'SELECT DISTINCT repeat_type FROM repeat_consensus');
}


=head2 fetch_by_dbID

  Arg [1]    : int $db_id
               The database identifier for the RepeatConsensus to obtain
  Example    : $repeat_consensus = $repeat_consensus_adaptor->fetch_by_dbID(4);
  Description: Obtains a RepeatConsensus object from the database via its
               primary key. 
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general, Bio::EnsEMBL::RepeatFeatureAdaptor
  Status     : Stable

=cut

sub fetch_by_dbID {
    my( $self, $db_id ) = @_;

    my ($rc) = @{$self->_generic_fetch("repeat_consensus_id = $db_id")};

    return $rc;
}



=head2 fetch_by_name

  Arg [1]    : string $name
               the name of the repeat consensus to obtain
  Example    : $rc = $repeat_consensus_adaptor->fetch_by_name('AluSx');
  Description: Obtains a repeat consensus from the database via its name
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub fetch_by_name {
    my( $self, $name ) = @_;

    my ($rc) = @{$self->_generic_fetch("repeat_name = '$name'")};

    return $rc;
}


=head2 fetch_by_name_class

  Arg [1]    : string $name
               the name of the repeat consensus to obtain
  Arg [2]    : string $class
               the class of the repeat consensus to obtain
  Example    : $rc = $repeat_consensus_adaptor->
                 fetch_by_name_class('AluSx', 'SINE/Alu');
  Description: Obtains a repeat consensus from the database
               via its name and class
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub fetch_by_name_class {
    my( $self, $name, $class ) = @_;


    my ($rc) = @{$self->_generic_fetch(qq{
      repeat_name  = '$name'
      AND repeat_class = '$class'
    })};

    return $rc;
}


=head2 fetch_all_by_class_seq

  Arg [1]    : string $class
               the class of the repeat consensus to obtain
  Arg [2]    : string $seq
               the sequence of the repeat consensus to obtain
  Example    : $rc = $repeat_consensus_adaptor->
                 fetch_all_by_class_seq('trf', 'ATGGTGTCA');
  Description: Obtains a repeat consensus from the database
               via its class and sequence
  Returntype : listREF of Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub fetch_all_by_class_seq {
    my( $self, $class, $seq ) = @_;

    return $self->_generic_fetch(qq{
            repeat_class     = '$class'
        AND repeat_consensus = '$seq'
    });
}


sub fetch_by_class_seq {
  deprecate('Use fetch_all_by_class_seq instead');
  fetch_all_by_class_seq(@_);
}


=head2 _generic_fetch

  Arg [1]    : string $where_clause
  Example    : none
  Description: PRIVATE used to create RepeatConsensus features from an 
               SQL constraint
  Returntype : listref of Bio::EnsEMBL::RepeatConsensus objects
  Exceptions : none
  Caller     : internal
  Status     : Stable

=cut

sub _generic_fetch {
    my( $self, $where_clause ) = @_;

    my( $repeat_consensus_id, $repeat_name, $repeat_class,$repeat_length,
        $repeat_consensus, $repeat_type );

    my $sth = $self->prepare(qq{
        SELECT repeat_consensus_id
          , repeat_name
          , repeat_class
          , repeat_type
          , repeat_consensus
        FROM repeat_consensus
        WHERE }. $where_clause);

    $sth->execute;
    $sth->bind_columns(
        \$repeat_consensus_id,
        \$repeat_name,
        \$repeat_class,
        \$repeat_type,
        \$repeat_consensus
        );

    
    my @consensi;
    while ($sth->fetch) {
      if ($repeat_consensus =~ /^(\d+)\(N\)$/) {
	$repeat_length = $1;
      } else {
	$repeat_length = CORE::length($repeat_consensus);
      }

      push @consensi, Bio::EnsEMBL::RepeatConsensus->new
          (-DBID => $repeat_consensus_id,
           -NAME => $repeat_name,
           -REPEAT_CLASS => $repeat_class,
           -REPEAT_TYPE => $repeat_type,
           -LENGTH => $repeat_length,
           -ADAPTOR => $self,
           -REPEAT_CONSENSUS => $repeat_consensus);
    }
    return \@consensi;
}


=head2 store

  Arg [1]    : list of Bio::EnsEMBL::RepeatConsensus @consensi
  Example    : $repeat_consensus_adaptor->store(@consensi);
  Description: stores a list of RepeatConsensus objects in the database
  Returntype : none
  Exceptions : none
  Caller     : ?
  Status     : Stable

=cut

sub store {
  my( $self, @consensi ) = @_;

  my $sth = $self->prepare(q{
    INSERT into repeat_consensus( repeat_consensus_id
          , repeat_name
          , repeat_class
          , repeat_type
          , repeat_consensus )
      VALUES (NULL, ?,?,?,?)
    });

  foreach my $rc (@consensi) {
    my $name  = $rc->name
      or throw("name not set");
    my $class = $rc->repeat_class
      or throw("repeat_class not set");
    my $type  = $rc->repeat_type();
    $type = "" unless defined $type;
    my $seq   = $rc->repeat_consensus
      or throw("repeat_consensus not set");

    $sth->bind_param(1,$name,SQL_VARCHAR);
    $sth->bind_param(2,$class,SQL_VARCHAR);
    $sth->bind_param(3,$type,SQL_VARCHAR);
    $sth->bind_param(4,$seq,SQL_LONGVARCHAR);

    $sth->execute();

    my $db_id = $sth->{'mysql_insertid'}
    or throw("Didn't get an insertid from the INSERT statement");

    $rc->dbID($db_id);
    $rc->adaptor($self);
  }
}

1;

__END__