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Summary

Bio::EnsEMBL::DBSQL::Funcgen::AnnotatedFeatureAdaptor - A database adaptor for fetching and
storing AnnotatedFeature objects.

Package variables

Included modules

Inherit

Bio::EnsEMBL::Funcgen::DBSQL::SetFeatureAdaptor

Synopsis

my $afa = $db->get_AnnotatedFeatureAdaptor();
my $features = $afa->fetch_all_by_Slice($slice);

Description

The AnnotatedFeatureAdaptor is a database adaptor for storing and retrieving
AnnotatedFeature objects.

Methods

Methods description

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns a list of columns to use for queries.
  Returntype : List of strings
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Args       : Hashref to be passed to AnnotatedFeature->new_fast()
  Example    : None
  Description: Construct a AnnotatedFeature object using quick and dirty new_fast.
  Returntype : Bio::EnsEMBL::Funcgen::AnnotatedFeature
  Exceptions : None
  Caller     : _objs_from_sth
  Status     : At Risk

  Arg [1]    : DBI statement handle object
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Creates AnnotatedFeature objects from an executed DBI statement
			   handle.
  Returntype : Listref of Bio::EnsEMBL::AnnotatedFeature objects
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Args       : None
  Example    : None
  Description: PROTECTED implementation of superclass abstract method.
               Returns the names and aliases of the tables to use for queries.
  Returntype : List of listrefs of strings
  Exceptions : None
  Caller     : Internal
  Status     : At Risk

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : Bio::EnsEMBL::Funcgen::Experiment
  Arg [3]    : (optional) string - logic name
  Example    : my $slice = $sa->fetch_by_region('chromosome', '1');
               my $features = $ofa->fetch_by_Slice_experiment_id($slice, $exp);
  Description: Retrieves a list of features on a given slice, specific for a given experiment.
  Returntype : Listref of Bio::EnsEMBL::AnnotatedFeature objects
  Exceptions : Throws if no Experiment object defined
  Caller     : General
  Status     : At Risk

  Arg [1]    : Bio::EnsEMBL::Slice
  Arg [2]    : Bio::EnsEMBL::Funcgen::Experiment
  Arg [3]    : (optional) string - logic name
  Example    : my $slice = $sa->fetch_by_region('chromosome', '1');
               my $features = $ofa->fetch_by_Slice_experiment_id($slice, $exp);
  Description: Retrieves a list of features on a given slice, specific for a given experiment.
  Returntype : Listref of Bio::EnsEMBL::AnnotatedFeature objects
  Exceptions : Throws if no Experiment object defined
  Caller     : General
  Status     : At Risk

  Args       : List of Bio::EnsEMBL::Funcgen::AnnotatedFeature objects
  Example    : $ofa->store(@features);
  Description: Stores given AnnotatedFeature objects in the database. Should only
               be called once per feature because no checks are made for
			   duplicates. Sets dbID and adaptor on the objects that it stores.
  Returntype : Listref of stored AnnotatedFeatures
  Exceptions : Throws if a list of AnnotatedFeature objects is not provided or if
               the Analysis, CellType and FeatureType objects are not attached or stored
  Caller     : General
  Status     : At Risk

Methods code

sub _columns {

  my $self = shift;
  
  return qw(
			af.annotated_feature_id  af.seq_region_id
			af.seq_region_start      af.seq_region_end
			af.seq_region_strand     af.feature_set_id
			af.display_label         af.score
	   );

}

sub _new_fast {

	my $self = shift;
	
	my $hash_ref = shift;
	return Bio::EnsEMBL::Funcgen::AnnotatedFeature->new_fast($hash_ref);

}

sub _objs_from_sth {

	my ($self, $sth, $mapper, $dest_slice) = @_;


	#For EFG this has to use a dest_slice from core/dnaDB whether specified or not.
	#So if it not defined then we need to generate one derived from the species_name and schema_build of the feature we're retrieving.

	# This code is ugly because caching is used to improve speed

	
	my ($sa, $seq_region_id);
	$sa = $dest_slice->adaptor->db->get_SliceAdaptor() if($dest_slice);#don't really need this if we're using DNADBSliceAdaptor?
	$sa ||= $self->db->get_SliceAdaptor();

 
	#Some of this in now probably overkill as we'll always be using the DNADB as the slice DB
	#Hence it should always be on the same coord system
	#my $aa = $self->db->get_AnalysisAdaptor();
	#my $ct_adaptor = $self->db->get_CellTypeAdaptor();
	my $fset_adaptor = $self->db->get_FeatureSetAdaptor();
	my @features;
	my (%fset_hash, %slice_hash, %sr_name_hash, %sr_cs_hash);

	my (
	    $annotated_feature_id,  $efg_seq_region_id,
	    $seq_region_start,      $seq_region_end,
	    $seq_region_strand,     $fset_id,
		$display_label,         $score
	);

	$sth->bind_columns(\$
					   annotated_feature_id,\$  efg_seq_region_id,\$
					   seq_region_start,\$      seq_region_end,\$
					   seq_region_strand,\$     fset_id,\$
					   display_label,\$         score
					  );


	#This needs doing properly!!
	#my $epsth = $self->prepare("SELECT experiment_id 
    #                                FROM experiment_prediction 
    #                                WHERE annotated_feature_id = ?");

	my $asm_cs;
	my $cmp_cs;
	my $asm_cs_name;
	my $asm_cs_vers;
	my $cmp_cs_name;
	my $cmp_cs_vers;
	if ($mapper) {
		$asm_cs      = $mapper->assembled_CoordSystem();
		$cmp_cs      = $mapper->component_CoordSystem();
		$asm_cs_name = $asm_cs->name();
		$asm_cs_vers = $asm_cs->version();
		$cmp_cs_name = $cmp_cs->name();
		$cmp_cs_vers = $cmp_cs->version();
	}

	my $dest_slice_start;
	my $dest_slice_end;
	my $dest_slice_strand;
	my $dest_slice_length;
	my $dest_slice_sr_name;
	if ($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_sr_name = $dest_slice->seq_region_name();
	}


  FEATURE: while ( $sth->fetch() ) {

	  #Need to build a slice adaptor cache here?
	  #Would only ever want to do this if we enable mapping between assemblies??
	  #Or if we supported the mapping between cs systems for a given schema_build, which would have to be handled by the core api
	  
	  #get core seq_region_id
	  $seq_region_id = $self->get_core_seq_region_id($efg_seq_region_id);
		
	  if(! $seq_region_id){
		warn "Cannot get slice for eFG seq_region_id $efg_seq_region_id\n".
		  "The region you are using is not present in the cuirrent dna DB";
		next;
	  }

	  #Get the FeatureSet object
	  $fset_hash{$fset_id} = $fset_adaptor->fetch_by_dbID($fset_id) if(! exists $fset_hash{$fset_id});
	  
   
	  # Get the slice object
	  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();
	  }
	  
	  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) {
		
		throw("Not yet implmented mapper, check equals are Funcgen calls too!");
		
	      ($sr_name, $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 $sr_name;
	      
	      # Get a slice in the coord system we just mapped to
	      if ( $asm_cs == $sr_cs || ( $cmp_cs != $sr_cs && $asm_cs->equals($sr_cs) ) ) {
		$slice = $slice_hash{"NAME:$sr_name:$cmp_cs_name:$cmp_cs_vers"}
		  ||= $sa->fetch_by_region($cmp_cs_name, $sr_name, undef, undef, undef, $cmp_cs_vers);
	      } else {
		$slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"}
		  ||= $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef, $asm_cs_vers);
	      }
	    }
	    
	    # If a destination slice was provided convert the coords
	    # If the destination slice starts at 1 and is forward strand, nothing needs doing
	    if ($dest_slice) {
	      unless ($dest_slice_start == 1 && $dest_slice_strand == 1) {
		if ($dest_slice_strand == 1) {
		  $seq_region_start = $seq_region_start - $dest_slice_start + 1;
		  $seq_region_end   = $seq_region_end   - $dest_slice_start + 1;
		} else {
		  my $tmp_seq_region_start = $seq_region_start;
		  $seq_region_start        = $dest_slice_end - $seq_region_end       + 1;
		  $seq_region_end          = $dest_slice_end - $tmp_seq_region_start + 1;
		  $seq_region_strand      *= -1;
		}
	      }
	      
	      # Throw away features off the end of the requested slice
	      next FEATURE if $seq_region_end < 1 || $seq_region_start > $dest_slice_length
		|| ( $dest_slice_sr_name ne $sr_name );
	      
	      $slice = $dest_slice;
	    }
	    

	  
	    push @features, $self->_new_fast( {
										   'start'          => $seq_region_start,
										   'end'            => $seq_region_end,
										   'strand'         => $seq_region_strand,
										   'slice'          => $slice,
										   'analysis'       => $fset_hash{$fset_id}->analysis(),
										   'adaptor'        => $self,
										   'dbID'           => $annotated_feature_id,
										   'score'          => $score,
										   'display_label'  => $display_label,
										   'feature_set'    => $fset_hash{$fset_id},
										  } );
	}
	
	return\@ features;

}

sub _tables {

  my $self = shift;
	
  return (
		  [ 'annotated_feature', 'af' ],
		  [ 'feature_set', 'fs'],#this is required for fetching on analysis or cell_type or feature_type
		 );
			#target?

}

sub fetch_all_by_Slice_Experiment {

  my ($self, $slice, $exp, $logic_name) = @_;
	

  if (! ($exp && $exp->isa("Bio::EnsEMBL::Funcgen::Experiment"))){
    throw("Need to pass a valid Bio::EnsEMBL::Funcgen::Experiment");
  }
  

  throw("Need to write DataSet and ResultSet to track back to experiment");
  
  
  my $constraint = qq( af.feature_set_id = fs.feature_set_id AND ep.experiment_id='$exp->dbID()' );
  
  $constraint = $self->_logic_name_to_constraint($constraint, $logic_name);
  
  return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint);

}

sub fetch_all_by_Slice_FeatureSet {

  my ($self, $slice, $fset) = @_;
	

  if (! ($fset && $fset->isa("Bio::EnsEMBL::Funcgen::FeatureSet"))){
    throw("Need to pass a valid Bio::EnsEMBL::Funcgen::FeatureSet");
  }
    
  my $constraint = qq( af.feature_set_id ='$fset->dbID()' );
  
  
  return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint);

}

sub store {

	my ($self, @pfs) = @_;
	
	if (scalar(@pfs) == 0) {
		throw('Must call store with a list of AnnotatedFeature objects');
	}
	
	my $sth = $self->prepare("
		INSERT INTO annotated_feature (
			seq_region_id,   seq_region_start,
			seq_region_end,  seq_region_strand,
            feature_set_id,  display_label, score
		) VALUES (?, ?, ?, ?, ?, ?, ?)
	");
	
	#my $epsth = $self->prepare("INSERT INTO experiment_prediction (
	#experiment_id, annotated_feature_id)
    #                          VALUES (?, ?)");
	
	my $db = $self->db();
	#my $analysis_adaptor = $db->get_AnalysisAdaptor();
	
  FEATURE: foreach my $pf (@pfs) {
		
		if( !ref $pf || !$pf->isa('Bio::EnsEMBL::Funcgen::AnnotatedFeature') ) {
			throw('Feature must be an AnnotatedFeature object');
		}
		
		if ( $pf->is_stored($db) ) {
			#does not accomodate adding Feature to >1 feature_set
			warning('AnnotatedFeature [' . $pf->dbID() . '] is already stored in the database');
			next FEATURE;
		}
		
		
		
		#Have to do this for Analysis separately due to inheritance, removed defined as constrained in Feature->new
		#Redundancy with Analysis in FeatureSet
		if ( ! $pf->analysis->is_stored($db)) {
			throw('A stored Bio::EnsEMBL::Analysis must be attached to the AnnotatedFeature objects to be stored.');
		}
		
		if (! $pf->feature_set->is_stored($db)) {
			throw('A stored Bio::EnsEMBL::Funcgen::FeatureSet must be attached to the AnnotatedFeature objects to be stored.');
		}

		#sanity check analysis matches feature_set analysis
		if($pf->analysis->dbID() != $pf->feature_set->analysis->dbID()){
			throw("AnnotatedFeature analysis(".$pf->analysis->logic_name().") does not match FeatureSet analysis(".$pf->feature_set->analysis->logic_name().")\n".
				  "Cannot store mixed analysis sets");
		}
		#Complex analysis to be stored as one in analysis table, or have feature_set_prediciton link table?
		#Or only have single analysis feature which can contribute to multi analysis "regulons"
		#Or can we have multiple entries in feature_set with the same id but different analyses?
		#This would still not be specific for each feature, nor would the annotated_feature analysis_id
		#reflect all the combined analyses.  Maybe just the one which contributed most?

		# Store the analysis if it has not been stored yet
		#$analysis_adaptor->store( $pf->analysis()) if ( !$pf->analysis->is_stored($db) );
		#could this potentially store the same on multiple times?

		my $seq_region_id;
		($pf, $seq_region_id) = $self->_pre_store($pf);
		
		$sth->bind_param(1, $seq_region_id,             SQL_INTEGER);
		$sth->bind_param(2, $pf->start(),               SQL_INTEGER);
		$sth->bind_param(3, $pf->end(),                 SQL_INTEGER);
		$sth->bind_param(4, $pf->strand(),              SQL_TINYINT);
		$sth->bind_param(5, $pf->feature_set->dbID(),   SQL_INTEGER);
		$sth->bind_param(6, $pf->display_label(),       SQL_VARCHAR);
		$sth->bind_param(7, $pf->score(),                SQL_DOUBLE);
		
		$sth->execute();
		$pf->dbID( $sth->{'mysql_insertid'} );

		#foreach my $exp_id(@{$pf->experiment_ids()}){
		#  $epsth->bind_param(1, $exp_id);
		#  $epsth->bind_param(2, $original->dbID());
		#  $epsth->execute();
		#}
		
		$pf->adaptor($self);
	}

  return\@ pfs;
}




1;

}

General documentation

This module was created by Nathan Johnson.
This module is part of the Ensembl project: /

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