RepeatFeatureAdaptor.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
 
=head1 CONTACT
 
  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
 
  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.
 
=cut
 
=head1 NAME
 
Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor
 
=head1 SYNOPSIS
 
  $rfa = $database_adaptor->get_RepeatFeatureAdaptor();
 
  my $repeat  = $rfa->fetch_by_dbID(1234);
  my @repeats = @{ $rfa->fetch_all_by_Slice($slice) };
 
=head1 DESCRIPTION
 
This is an adaptor for the retrieval and storage of RepeatFeature
objects from the database.  Most of the implementation is in the
superclass BaseFeatureAdaptor.
 
=head1 METHODS
 
=cut
 
package Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor;
 
use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::RepeatFeature;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::Scalar qw/wrap_array/;
 
use vars qw(@ISA);
 
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
 
 
=head2 fetch_all_by_Slice
 
  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Arg [2]    : (optional) string $logic_name
               Limits RepeatFeatures obtained to those having an Analysis with
               of the specified logic_name.  If no logic name is specified
               Repeats of all analysis types are retrieved.
  Arg [3]    : (optional) string/array $repeat_type
               Limits RepeatFeatures obtained to those of specified 
               repeat_type
  Example    : @rfeats = @{$rfa->fetch_all_by_Slice($slice, undef, 'Type II Transposons')};
               @rfeats = @{$rfa->fetch_all_by_Slice($slice, undef, ['Type II Transposons', 'RNA repeats'])};
  Description: Retrieves repeat features overlapping the area designated by
               the provided slice argument.  Returned features will be in
               in the same coordinate system as the provided slice and will
               have coordinates relative to the slice start.
  Returntype : reference to a list of Bio::EnsEMBL::RepeatFeatures.
  Exceptions : throw on bad argument
  Caller     : Slice::get_all_RepeatFeatures
  Status     : Stable
 
=cut
 
sub fetch_all_by_Slice {
  my $self = shift;
  my $slice = shift;
  my $logic_name = shift;
  my $repeat_type = shift;
 
  my $constraint = '';
 
  # MySQL was optimising the query the incorrect way when joining to
  # the repeat_consensus table on type
  $self->_straight_join(1);
 
  if($repeat_type) {
    my $rta = wrap_array($repeat_type);
    if(scalar(@{$rta}) > 1) {
      $constraint .= sprintf('rc.repeat_type IN (%s)', join(q{,}, map {"'${_}'"} @{$rta}));
    }
    else {
      $constraint .= "rc.repeat_type = '${repeat_type}'";      
    }
  }
 
  my $result =
    $self->fetch_all_by_Slice_constraint($slice,$constraint,$logic_name);
 
 
  $self->_straight_join(0);
 
  return $result;
}
 
 
#  _tablename
#
#   Arg [1]    : none
#   Example    : none
#   Description: PROTECTED Implementation of abstract superclass method to 
#                provide the name of the tables to query 
#   Returntype : string
#   Exceptions : none
#   Caller     : internal
 
 
sub _tables {
  my $self = shift;
 
  return (['repeat_feature', 'r'], ['repeat_consensus', 'rc']);
}
 
 
# _columns
#
#   Arg [1]    : none
#   Example    : none
#   Description: PROTECTED Implementation of abstract superclass method to 
#                provide the name of the columns to query 
#   Returntype : list of strings
#   Exceptions : none
#   Caller     : internal
 
sub _columns {
  my $self = shift;
 
  return qw (r.repeat_feature_id
         r.seq_region_id
         r.seq_region_start
         r.seq_region_end
         r.seq_region_strand
         r.repeat_consensus_id
         r.repeat_start
         r.repeat_end
         r.analysis_id
         r.score
         rc.repeat_name
         rc.repeat_class
         rc.repeat_type
         rc.repeat_consensus);
}
 
 
# _default_where_clause
#  Arg [1]    : none
#  Example    : none
#  Description: Overrides superclass method to provide an additional 
#               table joining constraint before the SQL query is performed.
#  Returntype : string
#  Exceptions : none
#  Caller     : generic_fetch
#
 
sub _default_where_clause {
  my $self = shift;
 
  return 'r.repeat_consensus_id = rc.repeat_consensus_id';
}
 
 
 
#  Description: PROTECTED implementation of abstract superclass method.
#               responsible for the creation of RepeatFeatures from a
#               hashref generated from an SQL query
 
sub _objs_from_sth {
  my ($self, $sth, $mapper, $dest_slice) = @_;
 
  #
  # This code is ugly because an attempt has been made to remove as many
  # function calls as possible for speed purposes.  Thus many caches and
  # a fair bit of gymnastics is used.
  #
 
  my $rca = $self->db()->get_RepeatConsensusAdaptor();
  my $sa = $self->db()->get_SliceAdaptor();
  my $aa = $self->db()->get_AnalysisAdaptor();
 
  my @features;
  my %rc_hash;
  my %analysis_hash;
  my %slice_hash;
  my %sr_name_hash;
  my %sr_cs_hash;
 
  my($repeat_feature_id, $seq_region_id, $seq_region_start, $seq_region_end,
     $seq_region_strand, $repeat_consensus_id, $repeat_start, $repeat_end,
     $analysis_id, $score, $repeat_name, $repeat_class, $repeat_type,
     $repeat_consensus);
 
  $sth->bind_columns( \$repeat_feature_id, \$seq_region_id, \$seq_region_start,
                      \$seq_region_end, \$seq_region_strand,
                      \$repeat_consensus_id, \$repeat_start,\$repeat_end,
                      \$analysis_id, \$score, \$repeat_name, \$repeat_class,
                      \$repeat_type, \$repeat_consensus );
 
  my $dest_slice_start;
  my $dest_slice_end;
  my $dest_slice_strand;
  my $dest_slice_length;
  my $dest_slice_cs;
  my $dest_slice_sr_name;
  my $dest_slice_sr_id;
  my $asma;
 
  if ($dest_slice) {
    $dest_slice_start   = $dest_slice->start();
    $dest_slice_end     = $dest_slice->end();
    $dest_slice_strand  = $dest_slice->strand();
    $dest_slice_length  = $dest_slice->length();
    $dest_slice_cs      = $dest_slice->coord_system();
    $dest_slice_sr_name = $dest_slice->seq_region_name();
    $dest_slice_sr_id   = $dest_slice->get_seq_region_id();
    $asma               = $self->db->get_AssemblyMapperAdaptor();
  }
 
  FEATURE: while($sth->fetch()) {
    #create a repeat consensus object
 
    my $rc = $rc_hash{$repeat_consensus_id} ||=
      Bio::EnsEMBL::RepeatConsensus->new_fast
          ({'dbID'             => $repeat_consensus_id,
            'adaptor'          => $rca,
            'name'             => $repeat_name,
            'repeat_class'     => $repeat_class,
            'repeat_type'      => $repeat_type,
            'repeat_consensus' => $repeat_consensus,
            'length'           => length($repeat_consensus)});
 
    #get the analysis object
    my $analysis = $analysis_hash{$analysis_id} ||= $aa->fetch_by_dbID($analysis_id);
    $analysis_hash{$analysis_id} = $analysis;
 
    #need to get the internal_seq_region, if present
    $seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
    my $slice = $slice_hash{"ID:".$seq_region_id};
 
    if (!$slice) {
      $slice                            = $sa->fetch_by_seq_region_id($seq_region_id);
      $slice_hash{"ID:".$seq_region_id} = $slice;
      $sr_name_hash{$seq_region_id}     = $slice->seq_region_name();
      $sr_cs_hash{$seq_region_id}       = $slice->coord_system();
    }
 
    #obtain a mapper if none was defined, but a dest_seq_region was
    if(!$mapper && $dest_slice && !$dest_slice_cs->equals($slice->coord_system)) {
      $mapper = $asma->fetch_by_CoordSystems($dest_slice_cs, $slice->coord_system);
    }
 
    my $sr_name = $sr_name_hash{$seq_region_id};
    my $sr_cs   = $sr_cs_hash{$seq_region_id};
 
    #
    # remap the feature coordinates to another coord system
    # if a mapper was provided
    #
 
    if ($mapper) {
 
      if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
        ($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) =
         $mapper->map($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs, 1, $dest_slice);
 
      } else {
        ($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) =
         $mapper->fastmap($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs);
      }
 
      #skip features that map to gaps or coord system boundaries
      next FEATURE if (!defined($seq_region_id));
 
      #get a slice in the coord system we just mapped to
      $slice = $slice_hash{"ID:".$seq_region_id} ||= $sa->fetch_by_seq_region_id($seq_region_id);
    }
 
    #
    # If a destination slice was provided convert the coords.
    #
    if (defined($dest_slice)) {
      my $seq_region_len = $dest_slice->seq_region_length();
 
      if ( $dest_slice_strand == 1 ) {
        $seq_region_start = $seq_region_start - $dest_slice_start + 1;
        $seq_region_end   = $seq_region_end - $dest_slice_start + 1;
 
        if ( $dest_slice->is_circular ) {
        # Handle circular chromosomes.
 
          if ( $seq_region_start > $seq_region_end ) {
            # Looking at a feature overlapping the chromosome origin.
 
            if ( $seq_region_end > $dest_slice_start ) {
              # Looking at the region in the beginning of the chromosome
              $seq_region_start -= $seq_region_len;
            }
            if ( $seq_region_end < 0 ) {
              $seq_region_end += $seq_region_len;
            }
          } else {
            if ($dest_slice_start > $dest_slice_end && $seq_region_end < 0) {
              # Looking at the region overlapping the chromosome
              # origin and a feature which is at the beginning of the
              # chromosome.
              $seq_region_start += $seq_region_len;
              $seq_region_end   += $seq_region_len;
            }
          }
        }
      } else {
 
        my $start = $dest_slice_end - $seq_region_end + 1;
        my $end = $dest_slice_end - $seq_region_start + 1;
 
        if ($dest_slice->is_circular()) {
 
          if ($dest_slice_start > $dest_slice_end) {
            # slice spans origin or replication
 
            if ($seq_region_start >= $dest_slice_start) {
              $end += $seq_region_len;
              $start += $seq_region_len if $seq_region_end > $dest_slice_start;
 
            } elsif ($seq_region_start <= $dest_slice_end) {
              # do nothing
            } elsif ($seq_region_end >= $dest_slice_start) {
              $start += $seq_region_len;
              $end += $seq_region_len;
 
            } elsif ($seq_region_end <= $dest_slice_end) {
              $end += $seq_region_len if $end < 0;
 
            } elsif ($seq_region_start > $seq_region_end) {
              $end += $seq_region_len;
            }
 
          } else {
 
            if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
              # do nothing
            } elsif ($seq_region_start > $seq_region_end) {
              if ($seq_region_start <= $dest_slice_end) {
                $start -= $seq_region_len;
              } elsif ($seq_region_end >= $dest_slice_start) {
                $end += $seq_region_len;
              }
            }
          }
        }
 
        $seq_region_start = $start;
        $seq_region_end = $end;
        $seq_region_strand *= -1;
 
      } ## end else [ if ( $dest_slice_strand...)]
 
      # Throw away features off the end of the requested slice or on
      # different seq_region.
      if ($seq_region_end < 1
          || $seq_region_start > $dest_slice_length
          || ($dest_slice_sr_id != $seq_region_id)) {
        next FEATURE;
      }
      $slice = $dest_slice;
    }
 
    # Finally, create the new RepeatFeature.
    push( @features,
          $self->_create_feature_fast( 'Bio::EnsEMBL::RepeatFeature', {
                                         'dbID' => $repeat_feature_id,
                                         'analysis' => $analysis,
                                         'start'  => $seq_region_start,
                                         'end'    => $seq_region_end,
                                         'strand' => $seq_region_strand,
                                         'score'  => $score,
                                         'hstart' => $repeat_start,
                                         'hend'   => $repeat_end,
                                         'repeat_consensus' => $rc,
                                         'adaptor'          => $self,
                                         'slice'            => $slice
                                       } ) );
 
  }
 
  return \@features;
}
 
 
=head2 store
 
  Arg [1]    : list of Bio::EnsEMBL::RepeatFeatures $repeat_feature_id
               the list of repeat features to store in the database
  Example    : $repeat_feature_adaptor->store(@repeat_features);
  Description: stores a repeat feature in the database
  Returntype : none
  Exceptions : if the repeat features do not have attached sequences 
               or if repeat_consensus are not present 
  Caller     : general
  Status     : Stable
 
=cut
 
sub store {
  my( $self, @repeats ) = @_;
 
  my $db = $self->db();
  my $rca = $db->get_RepeatConsensusAdaptor();
  my $sa  = $db->get_SliceAdaptor();
  my ($cons, $db_id);
 
  my $sth = $self->prepare(qq{
    INSERT into repeat_feature( repeat_feature_id
                , seq_region_id
                , seq_region_start
                , seq_region_end
                , seq_region_strand
                , repeat_consensus_id
                , repeat_start
                , repeat_end
                , score
                , analysis_id )
      VALUES(NULL, ?,?,?,?,?,?,?,?,?)
    });
 
 FEATURE: foreach my $rf (@repeats) {
    if(!ref($rf) || !$rf->isa('Bio::EnsEMBL::RepeatFeature')) {
      throw('Expected RepeatFeature argument not [' . ref($rf) .'].');
    }
 
    if($rf->is_stored($db)) {
      warning("RepeatFeature [".$rf->dbID."] is already stored in this DB.");
      next FEATURE;
    }
 
    my $cons = $rf->repeat_consensus();
    throw("Must have a RepeatConsensus attached") if(!defined($cons));
 
    # for tandem repeats - simply store consensus and repeat
    # one pair per hit. don't need to check consensi stored
    # already. consensus has name and class set to 'trf'
 
    if ($cons->repeat_class eq 'trf') {
 
      # Look for matches already stored
      my @match = @{$rca->fetch_all_by_class_seq('trf', $cons->repeat_consensus)};
      if (@match) {
        $cons->dbID($match[0]->dbID());
      }
      else {
        $rca->store($cons);
      }
 
    } elsif ($cons->repeat_class eq 'Simple_repeat') {
 
      my $rcon = $cons->name;
      $rcon =~ s/\((\S+)\)n/$1/;   # get repeat element
      $cons->repeat_consensus($rcon);
 
      # Look for matches already stored
      my $match = $rca->fetch_by_name_class($cons->name, 'Simple_repeat');
      if ($match) {
        $cons->dbID($match->dbID());
      }
      else {
        $rca->store($cons);
      }
 
    } else {
 
      # for other repeats - need to see if a consensus is stored already
      if(!$cons->dbID) {
        my $match = ($rca->fetch_by_name($cons->name));
    
        if($match) {
          #set the consensus dbID to be the same as the database one
          $cons->dbID($match->dbID());
        } else {
          # if we don't match a consensus already stored create a fake one 
          # and set consensus to 'N' as null seq not allowed
          # FIXME: not happy with this, but ho hum ...
          warning("Can't find " . $cons->name . "\n");
          $cons->repeat_consensus("N");
          $rca->store($cons);
        }
      }
    
      #if (@match > 1) {
      #multiple consensi were matched
      #  $self->warn(@match . " consensi for " . $cons->name . "\n");
      #}
    }
 
    my $slice = $rf->slice();
    if(!ref($slice) || !($slice->isa("Bio::EnsEMBL::Slice") or $slice->isa('Bio::EnsEMBL::LRGSlice'))) {
      throw("RepeatFeature cannot be stored without an associated slice.");
    }
 
    #store the analysis if it has not been stored yet
    if(!$rf->analysis->is_stored($db)) {
      $db->get_AnalysisAdaptor->store($rf->analysis());
    }
 
    my $original = $rf;
    my $seq_region_id;
    ($rf, $seq_region_id) = $self->_pre_store($rf);
 
    $sth->bind_param(1,$seq_region_id,SQL_INTEGER);
    $sth->bind_param(2,$rf->start,SQL_INTEGER);
    $sth->bind_param(3,$rf->end,SQL_INTEGER);
    $sth->bind_param(4,$rf->strand,SQL_TINYINT);
    $sth->bind_param(5,$rf->repeat_consensus->dbID,SQL_INTEGER);
    $sth->bind_param(6,$rf->hstart,SQL_INTEGER);
    $sth->bind_param(7,$rf->hend,SQL_INTEGER);
    $sth->bind_param(8,$rf->score,SQL_DOUBLE);
    $sth->bind_param(9,$rf->analysis->dbID,SQL_INTEGER);
 
    $sth->execute();
 
    my $db_id = $self->last_insert_id('repeat_feature_id', undef, 'repeat_feature')
      or throw("Didn't get an insertid from the INSERT statement");
 
    $original->dbID($db_id);
    $original->adaptor($self);
  }
}
 
 
=head2 list_dbIDs
 
  Arg [1]    : none
  Example    : @feature_ids = @{$repeat_feature_adaptor->list_dbIDs()};
  Description: Gets an array of internal ids for all repeat features in the current db
  Arg[1]     : <optional> int. not 0 for the ids to be sorted by the seq_region.
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable
 
=cut
 
sub list_dbIDs {
   my ($self, $ordered) = @_;
 
   return $self->_list_dbIDs("repeat_feature", undef, $ordered);
}
 
1;