Raw content of Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor - Retrieves supporting
features from the database.
=head1 SYNOPSIS
my $sfa =
$registry->get_adaptor( 'Human', 'Core', 'SupportingFeature' );
my @supporting_feats = @{ $sfa->fetch_all_by_Exon($exon) };
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::SupportingFeatureAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
#inherits from BaseAdaptor
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 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
=cut
sub fetch_all_by_Exon {
my ( $self, $exon ) = @_;
my $out = [];
unless($exon->dbID) {
warning("Cannot retrieve evidence for exon without dbID");
return [];
}
my $sth = $self->prepare("SELECT sf.feature_type, sf.feature_id
FROM supporting_feature sf
WHERE exon_id = ?");
$sth->bind_param(1,$exon->dbID,SQL_INTEGER);
$sth->execute();
my $prot_adp = $self->db->get_ProteinAlignFeatureAdaptor;
my $dna_adp = $self->db->get_DnaAlignFeatureAdaptor;
my $feature;
while(my ($type, $feature_id) = $sth->fetchrow){
if($type eq 'protein_align_feature'){
$feature = $prot_adp->fetch_by_dbID($feature_id);
} elsif($type eq 'dna_align_feature'){
$feature = $dna_adp->fetch_by_dbID($feature_id);
} else {
warning("Unknown feature type [$type]\n");
}
if(!$feature) {
warning("Supporting feature $type $feature_id does not exist in DB");
} else {
my $new_feature = $feature->transfer($exon->slice());
push @$out, $new_feature if( $new_feature );
}
}
$sth->finish();
return $out;
}
=head2 store
Arg [2] : Int $transID
The dbID of an EnsEMBL transcript to associate with
supporting features.
Arg [1] : 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 transcript with them
Returntype : none
Exceptions : thrown when invalid dbID is passed to this method
Caller : TranscriptAdaptor
Status : Stable
=cut
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;
}
1;
]]>