Raw content of Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor
<![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::ProteinFeatureAdaptor
=head1 SYNOPSIS
use Bio::EnsEMBL::Registry;
Bio::EnsEMBL::Registry->load_registry_from_db(
-host => 'ensembldb.ensembl.org',
-user => 'anonymous'
);
$pfa = Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
"proteinfeature" );
my @prot_feats = @{ $pfa->fetch_all_by_translation_id(1231) };
my $prot_feat = $pfa->fetch_by_dbID(523);
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::ProteinFeatureAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::ProteinFeature;
use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
use Data::Dumper;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_all_by_translation_id
Arg [1] : int $transl
the internal id of the translation corresponding to protein
whose features are desired
Example : @prot_feats = $prot_feat_adaptor->fetch_by_translation_id(1234);
Description: Gets all protein features present on a peptide using the
translations internal identifier. This method will return
an unsorted list of all protein_feature types. The feature
types may be distinguished using the logic name attribute of
the attached analysis objects.
Returntype : listref of Bio::EnsEMBL::ProteinFeatures
Exceptions : none
Caller : ?
Status : Stable
=cut
sub fetch_all_by_translation_id {
my($self,$translation_id) = @_;
if(!$translation_id) {
throw("translation_id argument is required\n");
}
my @features;
my $analysis_adaptor = $self->db()->get_AnalysisAdaptor();
my $sth = $self->prepare
("SELECT protein_feature_id, p.seq_start, p.seq_end, p.analysis_id, " .
" p.score, p.perc_ident, p.evalue, p.hit_start, p.hit_end, " .
" p.hit_name, x.display_label, i.interpro_ac " .
"FROM protein_feature p " .
"LEFT JOIN interpro AS i ON p.hit_name = i.id " .
"LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac " .
"WHERE p.translation_id = ?");
$sth->bind_param(1,$translation_id,SQL_INTEGER);
$sth->execute();
while( my $row = $sth->fetchrow_arrayref) {
my ($dbID, $start, $end, $analysisid, $score, $perc_id, $evalue, $hstart,
$hend,$hid,$desc, $interpro_ac) = @$row;
my $analysis = $analysis_adaptor->fetch_by_dbID($analysisid);
if(!$analysis) {
warning("Analysis with dbID=$analysisid does not exist\n" .
"but is referenced by ProteinFeature $dbID");
}
my $feat = Bio::EnsEMBL::ProteinFeature->new
(-DBID => $dbID,
-ADAPTOR => $self,
-SEQNAME => $translation_id,
-START => $start,
-END => $end,
-ANALYSIS => $analysis,
-PERCENT_ID => $perc_id,
-P_VALUE => $evalue,
-SCORE => $score,
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hid,
-IDESC => $desc,
-INTERPRO_AC => $interpro_ac);
push(@features,$feat);
}
$sth->finish();
return \@features;
}
=head2 fetch_by_dbID
Arg [1] : int $protfeat_id
the unique database identifier of the protein feature to obtain
Example : my $feature = $prot_feat_adaptor->fetch_by_dbID();
Description: Obtains a protein feature object via its unique id
Returntype : Bio::EnsEMBL::ProteinFeauture
Exceptions : none
Caller : ?
Status : Stable
=cut
sub fetch_by_dbID{
my ($self,$protfeat_id) = @_;
my $sth = $self->prepare(
"SELECT p.seq_start, p.seq_end, p.analysis_id, " .
" p.score, p.perc_ident, p.evalue, " .
" p.hit_start, p.hit_end, p.hit_name, " .
" x.display_label, i.interpro_ac " .
"FROM protein_feature p " .
"LEFT JOIN interpro AS i ON p.hit_name = i.id " .
"LEFT JOIN xref AS x ON x.dbprimary_acc = i.interpro_ac " .
"WHERE p.protein_feature_id = ?");
$sth->bind_param(1,$protfeat_id,SQL_INTEGER);
my $res = $sth->execute();
if($sth->rows == 0) {
$sth->finish();
return undef;
}
my ($start, $end, $analysis_id, $score, $perc_ident, $pvalue, $hstart,
$hend, $hseqname, $idesc, $interpro_ac) = $sth->fetchrow_array();
$sth->finish();
my $analysis = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id);
return Bio::EnsEMBL::ProteinFeature->new
(-ADAPTOR => $self,
-DBID => $protfeat_id,
-START => $start,
-END => $end,
-HSTART => $hstart,
-HEND => $hend,
-HSEQNAME => $hseqname,
-ANALYSIS => $analysis,
-SCORE => $score,
-P_VALUE => $pvalue,
-PERCENT_ID => $perc_ident,
-IDESC => $idesc,
-INTERPRO_AC => $interpro_ac);
}
=head2 store
Arg [1] : Bio::EnsEMBL::ProteinFeature $feature
The feature to be stored
Arg [2] : int $translation_id
Example : $protein_feature_adaptor->store($protein_feature);
Description: Stores a protein feature in the database
Returntype : int - the new internal identifier of the stored protein feature
Exceptions : thrown if arg is not a Bio::EnsEMBL:
Caller : none
Status : Stable
=cut
sub store {
my ($self,$feature, $translation_id) = @_;
if(!ref($feature) || !$feature->isa('Bio::EnsEMBL::ProteinFeature')) {
throw("ProteinFeature argument is required");
}
if(!$translation_id) {
deprecate("Calling ProteinFeatureAdaptor without a translation_id is " .
"deprecated. Pass a translation_id argument rather than " .
"setting the ProteinFeature seqname to be the translation " .
"id");
$translation_id = $feature->seqname();
}
my $db = $self->db();
if($feature->is_stored($db)) {
warning("ProteinFeature " . $feature->dbID() . " is already stored in " .
"this database - not storing again");
}
my $analysis = $feature->analysis();
if (!defined($analysis)) {
throw("Feature doesn't have analysis. Can't write to database");
}
if(!$analysis->is_stored($db)) {
$db->get_AnalysisAdaptor->store($analysis);
}
my $sth =
$self->prepare("INSERT INTO protein_feature " .
" SET translation_id = ?, " .
" seq_start = ?, ".
" seq_end = ?, ".
" analysis_id = ?, ".
" hit_start = ?, ".
" hit_end = ?, ".
" hit_name = ?, ".
" score = ?, ".
" perc_ident = ?, ".
" evalue = ?");
$sth->bind_param(1,$translation_id,SQL_INTEGER);
$sth->bind_param(2,$feature->start,SQL_INTEGER);
$sth->bind_param(3,$feature->end,SQL_INTEGER);
$sth->bind_param(4,$analysis->dbID,SQL_INTEGER);
$sth->bind_param(5,$feature->hstart,SQL_INTEGER);
$sth->bind_param(6,$feature->hend,SQL_INTEGER);
$sth->bind_param(7,$feature->hseqname,SQL_VARCHAR);
$sth->bind_param(8,$feature->score,SQL_DOUBLE);
$sth->bind_param(9,$feature->percent_id,SQL_FLOAT);
$sth->bind_param(10,$feature->p_value,SQL_DOUBLE);
$sth->execute();
my $dbID = $sth->{'mysql_insertid'};
$feature->adaptor($self);
$feature->dbID($dbID);
$sth->finish();
return $dbID;
}
sub fetch_by_translation_id {
deprecate("Use fetch_all_by_translation_id instead.");
fetch_all_by_translation_id(@_);
}
sub fetch_all_by_feature_and_dbID {
my $self = shift;
my $feature = shift;
my $translation_id = shift;
deprecate("Use fetch_all_by_translation_id instead.");
print STDERR "translation_id = $translation_id feature = $feature\n";
my $features = $self->fetch_all_by_translation_id($translation_id);
my @out;
foreach my $f (@$features) {
my $logic_name = lc($f->analysis->logic_name());
print STDERR "LOGIC_NAME = $logic_name | FEATURE = $feature\n";
push(@out, $f) if($logic_name eq lc($feature));
}
return \@out;
}
sub save {
my ($self, $features) = @_;
my @feats = @$features;
throw("Must call save with features") if( scalar(@feats) == 0 );
# my @tabs = $self->_tables;
# my ($tablename) = @{$tabs[0]};
my $tablename = 'protein_feature';
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
my $sql = qq{INSERT INTO $tablename (translation_id, seq_start, seq_end, hit_start, hit_end, hit_name, analysis_id, score, evalue, perc_ident, external_data) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)};
my $sth = $self->prepare($sql);
foreach my $feat ( @feats ) {
if( !ref $feat || !$feat->isa("Bio::EnsEMBL::ProteinFeature") ) {
throw("feature must be a Bio::EnsEMBL::ProteinFeature,". " not a [".ref($feat)."].");
}
if($feat->is_stored($db)) {
warning("ProteinFeature [".$feat->dbID."] is already stored" .
" in this database.");
next;
}
my $hstart = defined $feat->hstart ? $feat->hstart : $feat->start ;
my $hend = defined $feat->hend ? $feat->hend : $feat->end;
if(!defined($feat->analysis)) {
throw("An analysis must be attached to the features to be stored.");
}
#store the analysis if it has not been stored yet
if(!$feat->analysis->is_stored($db)) {
$analysis_adaptor->store($feat->analysis());
}
my $original = $feat;
my $extra_data = $feat->extra_data ? $self->dump_data($feat->extra_data) : '';
$sth->bind_param(1,$feat->translation_id,SQL_INTEGER);
$sth->bind_param(2,$feat->start,SQL_INTEGER);
$sth->bind_param(3,$feat->end,SQL_INTEGER);
$sth->bind_param(4,$hstart,SQL_INTEGER);
$sth->bind_param(5,$hend,SQL_INTEGER);
$sth->bind_param(6,$feat->hseqname,SQL_VARCHAR);
$sth->bind_param(7,$feat->analysis->dbID,SQL_INTEGER);
$sth->bind_param(8,$feat->score,SQL_DOUBLE);
$sth->bind_param(9,$feat->p_value,SQL_DOUBLE);
$sth->bind_param(10,$feat->percent_id,SQL_FLOAT);
$sth->bind_param(11,$extra_data,SQL_LONGVARCHAR);
$sth->execute();
$original->dbID($sth->{'mysql_insertid'});
$original->adaptor($self);
}
$sth->finish();
}
1;
]]>