Raw content of Bio::EnsEMBL::DBSQL::PredictionExonAdaptor
<![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::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
package Bio::EnsEMBL::DBSQL::PredictionExonAdaptor;
use vars qw( @ISA );
use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::PredictionExon;
use Bio::EnsEMBL::Utils::Exception qw( warning throw deprecate );
@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 = $sth->{'mysql_insertid'};
#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 $asm_cs;
my $cmp_cs;
my $asm_cs_vers;
my $asm_cs_name;
my $cmp_cs_vers;
my $cmp_cs_name;
if($mapper) {
$asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
$cmp_cs_vers = $cmp_cs->version();
}
my $dest_slice_start;
my $dest_slice_end;
my $dest_slice_strand;
my $dest_slice_length;
my $dest_slice_cs;
my $asma;
my $dest_slice_sr_name;
my $dest_slice_sr_id;
if($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};
my $dest_mapper = $mapper;
if(!$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} = $slice->coord_system();
}
#obtain a mapper if none was defined, but a dest_seq_region was
if(!$dest_mapper && $dest_slice &&
!$dest_slice_cs->equals($slice->coord_system)) {
$dest_mapper = $asma->fetch_by_CoordSystems($dest_slice_cs,
$slice->coord_system);
$asm_cs = $dest_mapper->assembled_CoordSystem();
$cmp_cs = $dest_mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
$cmp_cs_vers = $cmp_cs->version();
}
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($dest_mapper) {
($seq_region_id,$seq_region_start,$seq_region_end,$seq_region_strand) =
$dest_mapper->fastmap($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
# if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
# } else {
# $slice = $slice_hash{"NAME:$sr_name:$asm_cs_name:$asm_cs_vers"} ||=
# $sa->fetch_by_region($asm_cs_name, $sr_name, undef, undef, undef,
# $asm_cs_vers);
# }
}
#
# If a destination slice was provided convert the coords
# If the dest_slice starts at 1 and is foward strand, nothing needs doing
#
if($dest_slice) {
if($dest_slice_start != 1 || $dest_slice_strand != 1) {
if($dest_slice_strand == 1) {
$seq_region_start = $seq_region_start - $dest_slice_start + 1;
$seq_region_end = $seq_region_end - $dest_slice_start + 1;
} else {
my $tmp_seq_region_start = $seq_region_start;
$seq_region_start = $dest_slice_end - $seq_region_end + 1;
$seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
$seq_region_strand *= -1;
}
}
#throw away features off the end of the requested slice
if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
( $dest_slice_sr_id ne $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;
]]>