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Summary

Bio::EnsEMBL::Funcgen::DBSQL::SliceAdaptor - A database aware adaptor responsible for
the creation of Slices in the context of eFG objects.

Package variables

Included modules

Inherit

Bio::EnsEMBL::DBSQL::SliceAdaptor

Synopsis

  use Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor;
 

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

  $slice_adaptor = $db->get_SliceAdaptor();

  # get a slice on the entire chromosome X
  $gene_regulation_slice = $slice_adaptor->fetch_by_Gene_FeatureSets($gene, \@fsets);

Description

This module is simple wrapper class for the core SliceAdaptor, extending new
methods to generate Slices for eFG features associated with a given gene or transcript.

Methods

Methods description

  Arg [1]    : string - seq_region_name i.e. chromosome name.
  Arg [2]    : string - seq_region_start of current slice bound
  Arg [3]    : string - seq_region_end of current slice bound.
  Arg [4]    : Bio::EnsEMBL::Gene|Transcript|Translation
  Arg [5]    : arrayref - Bio::EnsEMBL::Funcgen::FeatureSet
  Example    : ($start, $end) = $self->_set_bounds_by_regulatory_feature_xref
                              ($trans_chr, $start, $end, $transcript, $fsets);
  Description: Internal method to set an xref Slice bounds given a list of
               FeatureSets.
  Returntype : List - ($start, $end);
  Exceptions : throw if incorrent args provided
  Caller     : self
  Status     : at risk

  Arg [1]    : Bio::EnsEMBL::Gene
  Example    : my $gene_reg_slice = $efg_slice_adaptor->fetch_by_gene($gene);
  Description: Fetches a slice by finding the associated regulatory
               elements associated with a given gene(and it's transcripts and 
               translations), and extending the gene feature slice to 
               encapsulate the associated regulatory elements.
  Returntype : Bio::EnsEMBL::Slice or undef
  Exceptions : throw if incorrent arg provided
  Caller     : General
  Status     : At risk

  Arg [1]    : Bio::EnsEMBL::Transcript
  Example    : my $trans_reg_slice = $efg_slice_adaptor->fetch_by_transcript($transcript);
  Description: Fetches a slice by finding the associated regulatory
               elements associated with a given transcript(and it's translation), and 
               extending the gene feature slice to encapsulate the associated regulatory 
               elements.
  Returntype : Bio::EnsEMBL::Slice or undef
  Exceptions : throw if incorrent arg provided
  Caller     : self
  Status     : at risk

Methods code

sub _set_bounds_by_xref_FeatureSets {

  my ($self, $chr, $start, $end, $obj, $fsets) = @_;

  my ($extdb_name, $efg_feature);
  my $dbe_adaptor = $self->efgdb->get_DBEntryAdaptor;


  #do we need to test for start/end/chr here?
  #Is implicit if we test for obj and fsets, but 
  #does not check if defined.

  #Set ext_dbname and validate obj
  #Do we need a central store for ensembl db names?

  


  if($obj->isa('Bio::EnsEMBL::Gene')){
	$extdb_name = 'ensembl_core_Gene';
  }
  elsif($obj->isa('Bio::EnsEMBL::Transcript')){
	$extdb_name = 'ensembl_core_Transcript';
  }
  elsif($obj->isa('Bio::EnsEMBL::Translation')){
	$extdb_name = 'ensembl_core_Translation';
  }
  else{
	throw('Currently only handles Ensembl Gene, Transcript and Translation xrefs');
  }


  #warn "Setting bounds by $obj ".$obj->stable_id;

  #Set which eFG features we want to look at.

  if(ref($fsets) ne 'ARRAY' || scalar(@$fsets) == 0){
	throw('Must define an array of Bio::EnsEMBL::FeatureSets to extend xref Slice bound. You passed: '.$fsets);
  }

  my %feature_set_types;

  foreach my $fset(@$fsets){
	$self->efgdb->is_stored_and_valid('Bio::EnsEMBL::Funcgen::FeatureSet', $fset);
	
	$feature_set_types{$fset->type} ||= [];
	push @{$feature_set_types{$fset->type}}, $fset;
  }


  #We can list the outer loop here and put in the BaseFeatureAdaptor, or possible storable as we do have FeatureType xrefs.
  #This would be useful for fetching all the efg features for a given xref and FeatureSets
  #Don't implement as a parent sub and call from here as this would mean looping through array twice.
  #Altho we could pass a code ref to do the filtering?
  #Just copy and paste for now to avoid obfuscation


  #Get xrefs for each eFG feature set type
  foreach my $fset_type(keys %feature_set_types){

	my $xref_method    = 'list_'.$fset_type.'_feature_ids_by_extid';
	#e.g. list_regulatory_feature_ids_by_extid

	my $adaptor_method = 'get_'.ucfirst($fset_type).'FeatureAdaptor';

	my $adaptor = $self->efgdb->$adaptor_method;

	my %feature_set_ids;
	map $feature_set_ids{$_->dbID} = 1, @{$feature_set_types{$fset_type}};

	#my $cnt = 0;


	#This should use fetch_all_by_external_name method

	foreach my $efg_feature(@{$adaptor->fetch_all_by_external_name($obj->stable_id, $extdb_name)}){
	  next if ! exists $feature_set_ids{$efg_feature->feature_set->dbID};
	  next if $efg_feature->seq_region_name ne $chr;
	  

	  #warn "found xref ".$efg_feature->display_label.' with start '.$efg_feature->seq_region_start;
	  #$cnt ++;
  	  
	  $start = $efg_feature->seq_region_start if $efg_feature->seq_region_start < $start;
	  $end   = $efg_feature->seq_region_end   if $efg_feature->seq_region_end   > $end;
	}
	
	#warn "Found $cnt $fset_type xrefs";

  }



  return ($start, $end);
}


1;

}

sub efgdb {

  my ($self, $efgdb) = @_;
  
  if($efgdb){

	if(! (ref($efgdb) && $efgdb->isa('Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor'))){
	  throw('Must provide a Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor');
	}
	
	$self->{'efgdb'} = $efgdb;	
  }

  return $self->{'efgdb'};

}

sub fetch_by_Gene_FeatureSets {

  my ($self, $gene, $fsets) = @_;

  if(! ( ref($gene) && $gene->isa('Bio::EnsEMBL::Gene'))){
    throw("You must pass a valid Bio::EnsEMBL::Gene object");
  }
  
  #Now we want to get all the eFG feature associated with this gene and build the slice
  #resitrict to RegFeats for now.
  my $cs_name      = $gene->slice->coord_system_name;
  my $gene_chr     = $gene->seq_region_name;
  my $start        = $gene->seq_region_start;
  my $end          = $gene->seq_region_end;
  

  ($start, $end) = $self->_set_bounds_by_xref_FeatureSets
	($gene_chr, $start, $end, $gene, $fsets);

  #Now need to do this for all transcripts and proteins too?
  
  foreach my $trans(@{$gene->get_all_Transcripts}){
	($start, $end) = $self->_set_bounds_by_xref_FeatureSets
	  ($gene_chr, $start, $end, $trans, $fsets);

	my $translation = $trans->translation;
	($start, $end) = $self->_set_bounds_by_xref_FeatureSets
	  ($gene_chr, $start, $end, $translation, $fsets) if $translation;
  }

  return $self->fetch_by_region($cs_name, $gene_chr, $start, $end, $gene->strand);

}

sub fetch_by_Transcript_FeatureSets {

  my ($self, $transcript, $fsets) = @_;


  if(! ( ref($transcript) && $transcript->isa('Bio::EnsEMBL::Transcript'))){
    throw("You must pass a valid Bio::EnsEMBL::Transcript object");
  }
  
  #Now we want to get all the eFG feature associated with this gene and build the slice
  #resitrict to RegFeats for now.
  my $cs_name   = $transcript->slice->coord_system_name;
  my $trans_chr = $transcript->seq_region_name;
  my $start     = $transcript->seq_region_start;
  my $end       = $transcript->seq_region_end;
  

  ($start, $end) = $self->_set_bounds_by_xref_FeatureSets
	($trans_chr, $start, $end, $transcript, $fsets);

  #Now need to do this for the protein too
  my $translation = $transcript->translation;
  ($start, $end) = $self->_set_bounds_by_xref_FeatureSets
	($trans_chr, $start, $end, $translation, $fsets) if $translation;


  return $self->fetch_by_region($cs_name, $trans_chr, $start, $end, $transcript->strand);
}

#Do we need fetch_by_translation?

}

sub new {

  my ($caller, $efgdb) = @_;

  my $class = ref($caller) || $caller;

  #Now have to reset the efg db to the dnadb
  #Does work using just efg.seq_region_id
  #But this is undesirable as we want to perform 
  #other non seq_region table style queries on core DB
  my $self = $class->SUPER::new($efgdb->dnadb);
  $self->efgdb($efgdb);
  return $self;

}

General documentation

This module is part of the Ensembl project
For more information email <ensembl-dev@ebi.ac.uk>