=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
Bio::EnsEMBL::DBSQL::PredictionExonAdaptor - Performs database interaction for
PredictionExons.
=head1 SYNOPSIS
$pea = $database_adaptor->get_PredictionExonAdaptor();
$pexon = $pea->fetch_by_dbID();
my $slice =
$database_adaptor->get_SliceAdaptor->fetch_by_region( 'X', 1, 1e6 );
my @pexons = @{ $pea->fetch_all_by_Slice($slice) };
=head1 METHODS
=cut
use vars qw( @ISA );
use strict;
use Bio::EnsEMBL::Utils::Exception qw( warning throw );
@ISA = qw( Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor );
#_tables
#
# Arg [1] : none
# Example : none
# Description: PROTECTED implementation of superclass abstract method
# returns the names, aliases of the tables to use for queries
# Returntype : list of listrefs of strings
# Exceptions : none
# Caller : internal
#
sub _tables {
return ([ 'prediction_exon', 'pe' ] );
}
#_columns
#
# Arg [1] : 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
sub _columns {
my $self = shift;
return qw( pe.prediction_exon_id
pe.seq_region_id
pe.seq_region_start
pe.seq_region_end
pe.seq_region_strand
pe.start_phase
pe.score
pe.p_value );
}
# _final_clause
#
# Arg [1] : none
# Example : none
# Description: PROTECTED implementation of superclass abstract method
# returns a default end for the SQL-query (ORDER BY)
# Returntype : string
# Exceptions : none
# Caller : internal
sub _final_clause {
return "ORDER BY pe.prediction_transcript_id, pe.exon_rank";
}
=head2 fetch_all_by_PredictionTranscript
Arg [1] : Bio::EnsEMBL::PredcitionTranscript $transcript
Example : none
Description: Retrieves all Exons for the Transcript in 5-3 order
Returntype : listref Bio::EnsEMBL::Exon on Transcript slice
Exceptions : throws if transcript does not have a slice
Caller : Transcript->get_all_Exons()
Status : Stable
=cut
sub fetch_all_by_PredictionTranscript {
my ( $self, $transcript ) = @_;
my $constraint = "pe.prediction_transcript_id = ".$transcript->dbID();
# use 'keep_all' option to keep exons that are off end of slice
my $tslice = $transcript->slice();
my $slice;
if(!$tslice) {
throw("Transcript must have attached slice to retrieve exons.");
}
# use a small slice the same size as the prediction transcript
$slice = $self->db->get_SliceAdaptor->fetch_by_Feature($transcript);
my $exons = $self->fetch_all_by_Slice_constraint($slice, $constraint);
# remap exon coordinates if necessary
if($slice->name() ne $tslice->name()) {
my @out;
foreach my $ex (@$exons) {
push @out, $ex->transfer($tslice);
}
$exons = \@out;
}
return $exons;
}
=head2 store
Arg [1] : Bio::EnsEMBL::PredictionExon $exon
The exon to store in this database
Arg [2] : int $prediction_transcript_id
The internal identifier of the prediction exon that that this
exon is associated with.
Arg [3] : int $rank
The rank of the exon in the transcript (starting at 1)
Example : $pexon_adaptor->store($pexon, 1211, 2);
Description: Stores a PredictionExon in the database
Returntype : none
Exceptions : thrown if exon does not have a slice attached
or if $exon->start, $exon->end, $exon->strand, or $exon->phase
are not defined or if $exon is not a Bio::EnsEMBL::PredictionExon
Caller : general
Status : Stable
=cut
sub store {
my ( $self, $pexon, $pt_id, $rank ) = @_;
if(!ref($pexon) || !$pexon->isa('Bio::EnsEMBL::PredictionExon') ) {
throw("Expected PredictionExon argument");
}
throw("Expected PredictionTranscript id argument.") if(!$pt_id);
throw("Expected rank argument.") if(!$rank);
my $db = $self->db();
if($pexon->is_stored($db)) {
warning('PredictionExon is already stored in this DB.');
return $pexon->dbID();
}
if( ! $pexon->start || ! $pexon->end ||
! $pexon->strand || ! defined $pexon->phase ) {
throw("PredictionExon does not have all attributes to store.\n" .
"start, end, strand and phase attributes must be set.");
}
#maintain reference to original passed-in prediction exon
my $original = $pexon;
my $seq_region_id;
($pexon, $seq_region_id) = $self->_pre_store($pexon);
my $sth = $db->dbc->prepare
("INSERT into prediction_exon (prediction_transcript_id, exon_rank, " .
"seq_region_id, seq_region_start, seq_region_end, " .
"seq_region_strand, start_phase, score, p_value) " .
"VALUES ( ?, ?, ?, ?, ?, ?, ?, ?, ? )");
$sth->bind_param(1,$pt_id,SQL_INTEGER);
$sth->bind_param(2,$rank,SQL_SMALLINT);
$sth->bind_param(3,$seq_region_id,SQL_INTEGER);
$sth->bind_param(4,$pexon->start,SQL_INTEGER);
$sth->bind_param(5,$pexon->end,SQL_INTEGER);
$sth->bind_param(6,$pexon->strand,SQL_TINYINT);
$sth->bind_param(7,$pexon->phase,SQL_TINYINT);
$sth->bind_param(8,$pexon->score,SQL_DOUBLE);
$sth->bind_param(9,$pexon->p_value,SQL_DOUBLE);
$sth->execute();
my $dbID = $self->last_insert_id('prediction_transcript_id', undef, 'prediction_transcript');
#set the adaptor and dbID of the object they passed in
$original->dbID($dbID);
$original->adaptor($self);
return $dbID;
}
=head2 remove
Arg [1] : Bio::EnsEMBL::PredictionExon $exon
the exon to remove from the database
Example : $exon_adaptor->remove($exon);
Description: Removes an exon from the database
Returntype : none
Exceptions : none
Caller : general
Status : Stable
=cut
sub remove {
my $self = shift;
my $pexon = shift;
my $db = $self->db();
if(!$pexon->is_stored($db)) {
warning('PredictionExon is not in this DB - not removing');
return undef;
}
my $sth = $self->prepare(
"DELETE FROM prediction_exon WHERE prediction_exon_id = ?");
$sth->bind_param( 1, $pexon->dbID, SQL_INTEGER );
$sth->execute();
$pexon->dbID(undef);
$pexon->adaptor(undef);
}
=head2 list_dbIDs
Arg [1] : none
Example : @exon_ids = @{$exon_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all exons in the current db
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller : ?
Status : Stable
=cut
sub list_dbIDs {
my ($self,$ordered) = @_;
return $self->_list_dbIDs("prediction_exon",undef, $ordered);
}
#_objs_from_sth
# Arg [1] : Hashreference $hashref
# Example : none
# Description: PROTECTED implementation of abstract superclass method.
# responsible for the creation of Genes
# Returntype : listref of Bio::EnsEMBL::Genes in target coordinate system
# Exceptions : none
# Caller : internal
#
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
#
# This code is ugly because an attempt has been made to remove as many
# function calls as possible for speed purposes. Thus many caches and
# a fair bit of gymnastics is used.
#
my $sa = $self->db()->get_SliceAdaptor();
my @exons;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my(
$prediction_exon_id, $seq_region_id,
$seq_region_start, $seq_region_end, $seq_region_strand,
$start_phase, $score, $p_value);
$sth->bind_columns(\(
$prediction_exon_id, $seq_region_id,
$seq_region_start, $seq_region_end, $seq_region_strand,
$start_phase, $score, $p_value));
my $dest_slice_start;
my $dest_slice_end;
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_cs;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
my $asma;
if ($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_cs = $dest_slice->coord_system();
$dest_slice_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id();
$asma = $self->db->get_AssemblyMapperAdaptor();
}
FEATURE: while($sth->fetch()) {
#need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
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} = $slice->coord_system();
}
#obtain a mapper if none was defined, but a dest_seq_region was
if(!$mapper && $dest_slice && !$dest_slice_cs->equals($slice->coord_system)) {
$mapper = $asma->fetch_by_CoordSystems($dest_slice_cs, $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) {
if (defined $dest_slice && $mapper->isa('Bio::EnsEMBL::ChainedAssemblyMapper') ) {
($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) =
$mapper->map($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs, 1, $dest_slice);
} else {
($seq_region_id, $seq_region_start, $seq_region_end, $seq_region_strand) =
$mapper->fastmap($sr_name, $seq_region_start, $seq_region_end, $seq_region_strand, $sr_cs);
}
#skip features that map to gaps or coord system boundaries
next FEATURE if (!defined($seq_region_id));
#get a slice in the coord system we just mapped to
$slice = $slice_hash{"ID:".$seq_region_id} ||= $sa->fetch_by_seq_region_id($seq_region_id);
}
#
# If a destination slice was provided convert the coords.
#
if (defined($dest_slice)) {
my $seq_region_len = $dest_slice->seq_region_length();
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;
if ( $dest_slice->is_circular ) {
# Handle circular chromosomes.
if ( $seq_region_start > $seq_region_end ) {
# Looking at a feature overlapping the chromosome origin.
if ( $seq_region_end > $dest_slice_start ) {
# Looking at the region in the beginning of the chromosome
$seq_region_start -= $seq_region_len;
}
if ( $seq_region_end < 0 ) {
$seq_region_end += $seq_region_len;
}
} else {
if ($dest_slice_start > $dest_slice_end && $seq_region_end < 0) {
# Looking at the region overlapping the chromosome
# origin and a feature which is at the beginning of the
# chromosome.
$seq_region_start += $seq_region_len;
$seq_region_end += $seq_region_len;
}
}
}
} else {
my $start = $dest_slice_end - $seq_region_end + 1;
my $end = $dest_slice_end - $seq_region_start + 1;
if ($dest_slice->is_circular()) {
if ($dest_slice_start > $dest_slice_end) {
# slice spans origin or replication
if ($seq_region_start >= $dest_slice_start) {
$end += $seq_region_len;
$start += $seq_region_len if $seq_region_end > $dest_slice_start;
} elsif ($seq_region_start <= $dest_slice_end) {
# do nothing
} elsif ($seq_region_end >= $dest_slice_start) {
$start += $seq_region_len;
$end += $seq_region_len;
} elsif ($seq_region_end <= $dest_slice_end) {
$end += $seq_region_len if $end < 0;
} elsif ($seq_region_start > $seq_region_end) {
$end += $seq_region_len;
}
} else {
if ($seq_region_start <= $dest_slice_end and $seq_region_end >= $dest_slice_start) {
# do nothing
} elsif ($seq_region_start > $seq_region_end) {
if ($seq_region_start <= $dest_slice_end) {
$start -= $seq_region_len;
} elsif ($seq_region_end >= $dest_slice_start) {
$end += $seq_region_len;
}
}
}
}
$seq_region_start = $start;
$seq_region_end = $end;
$seq_region_strand *= -1;
} ## end else [ if ( $dest_slice_strand...)]
# Throw away features off the end of the requested slice or on
# different seq_region.
if ($seq_region_end < 1
|| $seq_region_start > $dest_slice_length
|| ($dest_slice_sr_id != $seq_region_id)) {
next FEATURE;
}
$slice = $dest_slice;
}
# Finally, create the new PredictionExon.
push( @exons,
$self->_create_feature( 'Bio::EnsEMBL::PredictionExon', {
'-start' => $seq_region_start,
'-end' => $seq_region_end,
'-strand' => $seq_region_strand,
'-adaptor' => $self,
'-slice' => $slice,
'-dbID' => $prediction_exon_id,
'-phase' => $start_phase,
'-score' => $score,
'-p_value' => $p_value
} ) );
}
return \@exons;
}
1;