ensembl-hive 2.8.1

Inheritance diagram for Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor:

Public Member Functions
public List	fetch_all_by_Exon ()

public void	store ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

Synopsis

my $sfa =
  $registry->get_adaptor( 'Human', 'Core', 'SupportingFeature' );
 
my @supporting_feats = @{ $sfa->fetch_all_by_Exon($exon) };

Definition at line 15 of file SupportingFeatureAdaptor.pm.

Member Function Documentation

◆ fetch_all_by_Exon()

public List Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor::fetch_all_by_Exon ( )

  Arg [1]    : Bio::EnsEMBL::Exon $exon 
               The exon to fetch supporting features.
  Example    :

@sfs =

@{ $supporting_feat_adaptor->fetch_all_by_Exon($exon) };

  Description: Retrieves supporting features (evidence) for a given
               exon.
  Returntype : List of Bio::EnsEMBL::BaseAlignFeatures in the same
               coordinate system as the $exon argument
  Exceptions : Warning if $exon is not in the database (i.e. dbID
               not defined).
               Throw if a retrieved supporting feature is of unknown
               type.
  Caller     : Bio::EnsEMBL::Exon
  Status     : Stable

Code:

click to view

◆ store()

public void Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor::store ( )

  Arg [1]    : Int $exonsID
               The dbID of an EnsEMBL exon to associate with
               supporting features.
  Arg [2]    : Ref to array of Bio::EnsEMBL::BaseAlignFeature
               (the support)
  Example    :

$sfa->store($exon_id, \@features);

  Description: Stores a set of alignment features and associates an
               EnsEMBL exon with them
  Returntype : none
  Exceptions : thrown when invalid dbID is passed to this method
  Caller     : TranscriptAdaptor
  Status     : Stable

Code:

click to view

sub store {
  my ( $self, $exon_dbID, $aln_objs ) = @_;
 
  my $pep_check_sql = 
      "SELECT protein_align_feature_id " . 
      "FROM protein_align_feature " . 
      "WHERE seq_region_id = ? " . 
      "AND   seq_region_start = ? " . 
      "AND   seq_region_end   = ? " .
      "AND   seq_region_strand = ? " . 
      "AND   hit_name = ? " . 
      "AND   hit_start = ? " . 
      "AND   hit_end   = ? " . 
      "AND   analysis_id = ? " . 
      "AND   cigar_line = ? ";
 
  my $dna_check_sql = 
      "SELECT dna_align_feature_id " . 
      "FROM dna_align_feature " . 
      "WHERE seq_region_id = ? " . 
      "AND   seq_region_start = ? " . 
      "AND   seq_region_end   = ? " .
      "AND   seq_region_strand = ? " . 
      "AND   hit_name = ? " . 
      "AND   hit_start = ? " . 
      "AND   hit_end   = ? " . 
      "AND   analysis_id = ? " . 
      "AND   cigar_line = ? " . 
      "AND   hit_strand = ? ";
 
  my $assoc_check_sql = 
      "SELECT * " .  
      "FROM  supporting_feature " . 
      "WHERE exon_id = $exon_dbID " . 
      "AND   feature_type = ? " . 
      "AND   feature_id   = ? ";
 
  my $assoc_write_sql = "INSERT into supporting_feature " . 
      "(exon_id, feature_id, feature_type) " . 
      "values(?, ?, ?)";
 
  my $pep_check_sth = $self->prepare($pep_check_sql);
  my $dna_check_sth = $self->prepare($dna_check_sql);
  my $assoc_check_sth = $self->prepare($assoc_check_sql);
  my $sf_sth = $self->prepare($assoc_write_sql);
 
  my $dna_adaptor = $self->db->get_DnaAlignFeatureAdaptor();
  my $pep_adaptor = $self->db->get_ProteinAlignFeatureAdaptor();
 
  foreach my $f (@$aln_objs) {
    # check that the feature is in toplevel coords
 
    if($f->slice->start != 1 || $f->slice->strand != 1) {
    #move feature onto a slice of the entire seq_region
      my $tls = $self->db->get_sliceAdaptor->fetch_by_region($f->slice->coord_system->name(),
                                                             $f->slice->seq_region_name(),
                                                             undef, #start
                                                             undef, #end
                                                             undef, #strand
                                                             $f->slice->coord_system->version());
      $f = $f->transfer($tls);
 
      if(!$f) {
        throw('Could not transfer Feature to slice of ' .
              'entire seq_region prior to storing');
      }
    }
 
    if(!$f->isa("Bio::EnsEMBL::BaseAlignFeature")){
      throw("$f must be an align feature otherwise" .
            "it can't be stored");
    }
    
    my ($sf_dbID, $type, $adap, $check_sth);
    
    my @check_args = ($self->db->get_SliceAdaptor->get_seq_region_id($f->slice),
                      $f->start,
                      $f->end,
                      $f->strand,
                      $f->hseqname,
                      $f->hstart,
                      $f->hend,
                      $f->analysis->dbID,
                      $f->cigar_string);
 
    if($f->isa("Bio::EnsEMBL::DnaDnaAlignFeature")){
      $adap = $dna_adaptor;      
      $check_sth = $dna_check_sth;
      $type = 'dna_align_feature';
      push @check_args, $f->hstrand;
    } elsif($f->isa("Bio::EnsEMBL::DnaPepAlignFeature")){
      $adap = $pep_adaptor;
      $check_sth = $pep_check_sth;
      $type = 'protein_align_feature';
    } else {
      warning("Supporting feature of unknown type. Skipping : [$f]\n");
      next;
    }
 
    $check_sth->execute(@check_args);
    $sf_dbID = $check_sth->fetchrow_array;
    if (not $sf_dbID) {
      $adap->store($f);
      $sf_dbID = $f->dbID;
    }
 
    # now check association
    $assoc_check_sth->execute($type,
                              $sf_dbID);
    if (not $assoc_check_sth->fetchrow_array) {    
      $sf_sth->bind_param(1, $exon_dbID, SQL_INTEGER);
      $sf_sth->bind_param(2, $sf_dbID, SQL_INTEGER);
      $sf_sth->bind_param(3, $type, SQL_VARCHAR);
      $sf_sth->execute();
    }
  }
 
  $dna_check_sth->finish;
  $pep_check_sth->finish;
  $assoc_check_sth->finish;
  $sf_sth->finish;
  
}

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/DBSQL/SupportingFeatureAdaptor.pm

Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor::store

public void store()

Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor::fetch_all_by_Exon

public List fetch_all_by_Exon()

Bio
EnsEMBL
DBSQL
SupportingFeatureAdaptor
Generated on Mon Sep 29 2025 11:36:50 for ensembl-hive by 1.8.17