Raw content of Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor
<![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::RepeatFeatureAdaptor
=head1 SYNOPSIS
$rfa = $database_adaptor->get_RepeatFeatureAdaptor();
my $repeat = $rfa->fetch_by_dbID(1234);
my @repeats = @{ $rfa->fetch_all_by_Slice($slice) };
=head1 DESCRIPTION
This is an adaptor for the retrieval and storage of RepeatFeature
objects from the database. Most of the implementation is in the
superclass BaseFeatureAdaptor.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::RepeatFeatureAdaptor;
use strict;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use Bio::EnsEMBL::RepeatFeature;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
=head2 fetch_all_by_Slice
Arg [1] : Bio::EnsEMBL::Slice $slice
Arg [2] : (optional) string $logic_name
Limits RepeatFeatures obtained to those having an Analysis with
of the specified logic_name. If no logic name is specified
Repeats of all analysis types are retrieved.
Arg [3] : (optional) string $repeat_type
Limits RepeatFeatures obtained to those of specified repeat_type
Example : @rfeats = @{$rfa->fetch_all_by_Slice($slice, undef, 'LTR')};
Description: Retrieves repeat features overlapping the area designated by
the provided slice argument. Returned features will be in
in the same coordinate system as the provided slice and will
have coordinates relative to the slice start.
Returntype : reference to a list of Bio::EnsEMBL::RepeatFeatures.
Exceptions : throw on bad argument
Caller : Slice::get_all_RepeatFeatures
Status : Stable
=cut
sub fetch_all_by_Slice {
my $self = shift;
my $slice = shift;
my $logic_name = shift;
my $repeat_type = shift;
my $constraint = '';
# MySQL was optimising the query the incorrect way when joining to
# the repeat_consensus table on type
$self->_straight_join(1);
if($repeat_type) {
$constraint .= "rc.repeat_type =\"$repeat_type\"";
}
my $result =
$self->fetch_all_by_Slice_constraint($slice,$constraint,$logic_name);
$self->_straight_join(0);
return $result;
}
# _tablename
#
# Arg [1] : none
# Example : none
# Description: PROTECTED Implementation of abstract superclass method to
# provide the name of the tables to query
# Returntype : string
# Exceptions : none
# Caller : internal
sub _tables {
my $self = shift;
return (['repeat_feature', 'r'], ['repeat_consensus', 'rc']);
}
# _columns
#
# Arg [1] : none
# Example : none
# Description: PROTECTED Implementation of abstract superclass method to
# provide the name of the columns to query
# Returntype : list of strings
# Exceptions : none
# Caller : internal
sub _columns {
my $self = shift;
return qw (r.repeat_feature_id
r.seq_region_id
r.seq_region_start
r.seq_region_end
r.seq_region_strand
r.repeat_consensus_id
r.repeat_start
r.repeat_end
r.analysis_id
r.score
rc.repeat_name
rc.repeat_class
rc.repeat_type
rc.repeat_consensus);
}
# _default_where_clause
# Arg [1] : none
# Example : none
# Description: Overrides superclass method to provide an additional
# table joining constraint before the SQL query is performed.
# Returntype : string
# Exceptions : none
# Caller : generic_fetch
#
sub _default_where_clause {
my $self = shift;
return 'r.repeat_consensus_id = rc.repeat_consensus_id';
}
# Description: PROTECTED implementation of abstract superclass method.
# responsible for the creation of RepeatFeatures from a
# hashref generated from an SQL query
sub _objs_from_sth {
my ($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 $rca = $self->db()->get_RepeatConsensusAdaptor();
my $sa = $self->db()->get_SliceAdaptor();
my $aa = $self->db->get_AnalysisAdaptor();
my @features;
my %rc_hash;
my %analysis_hash;
my %slice_hash;
my %sr_name_hash;
my %sr_cs_hash;
my($repeat_feature_id, $seq_region_id, $seq_region_start, $seq_region_end,
$seq_region_strand, $repeat_consensus_id, $repeat_start, $repeat_end,
$analysis_id, $score, $repeat_name, $repeat_class, $repeat_type,
$repeat_consensus);
$sth->bind_columns( \$repeat_feature_id, \$seq_region_id, \$seq_region_start,
\$seq_region_end, \$seq_region_strand,
\$repeat_consensus_id, \$repeat_start,\$repeat_end,
\$analysis_id, \$score, \$repeat_name, \$repeat_class,
\$repeat_type, \$repeat_consensus );
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_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_sr_name = $dest_slice->seq_region_name();
$dest_slice_sr_id = $dest_slice->get_seq_region_id();
}
FEATURE: while($sth->fetch()) {
#create a repeat consensus object
my $rc = $rc_hash{$repeat_consensus_id} ||=
Bio::EnsEMBL::RepeatConsensus->new_fast
({'dbID' => $repeat_consensus_id,
'adaptor' => $rca,
'name' => $repeat_name,
'repeat_class' => $repeat_class,
'repeat_type' => $repeat_type,
'repeat_consensus' => $repeat_consensus,
'length' => length($repeat_consensus)});
#get the analysis object
my $analysis = $analysis_hash{$analysis_id} ||=
$aa->fetch_by_dbID($analysis_id);
#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();
}
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($mapper) {
($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
# 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 RepeatFeature.
push( @features,
$self->_create_feature_fast( 'Bio::EnsEMBL::RepeatFeature', {
'dbID' => $repeat_feature_id,
'analysis' => $analysis,
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'score' => $score,
'hstart' => $repeat_start,
'hend' => $repeat_end,
'repeat_consensus' => $rc,
'adaptor' => $self,
'slice' => $slice
} ) );
}
return \@features;
}
=head2 store
Arg [1] : list of Bio::EnsEMBL::RepeatFeatures $repeat_feature_id
the list of repeat features to store in the database
Example : $repeat_feature_adaptor->store(@repeat_features);
Description: stores a repeat feature in the database
Returntype : none
Exceptions : if the repeat features do not have attached sequences
or if repeat_consensus are not present
Caller : general
Status : Stable
=cut
sub store {
my( $self, @repeats ) = @_;
my $db = $self->db();
my $rca = $db->get_RepeatConsensusAdaptor();
my $sa = $db->get_SliceAdaptor();
my ($cons, $db_id);
my $sth = $self->prepare(qq{
INSERT into repeat_feature( repeat_feature_id
, seq_region_id
, seq_region_start
, seq_region_end
, seq_region_strand
, repeat_consensus_id
, repeat_start
, repeat_end
, score
, analysis_id )
VALUES(NULL, ?,?,?,?,?,?,?,?,?)
});
FEATURE: foreach my $rf (@repeats) {
if(!ref($rf) || !$rf->isa('Bio::EnsEMBL::RepeatFeature')) {
throw('Expected RepeatFeature argument not [' . ref($rf) .'].');
}
if($rf->is_stored($db)) {
warning("RepeatFeature [".$rf->dbID."] is already stored in this DB.");
next FEATURE;
}
my $cons = $rf->repeat_consensus();
throw("Must have a RepeatConsensus attached") if(!defined($cons));
# for tandem repeats - simply store consensus and repeat
# one pair per hit. don't need to check consensi stored
# already. consensus has name and class set to 'trf'
if ($cons->repeat_class eq 'trf') {
# Look for matches already stored
my @match = @{$rca->fetch_all_by_class_seq('trf', $cons->repeat_consensus)};
if (@match) {
$cons->dbID($match[0]->dbID());
}
else {
$rca->store($cons);
}
} elsif ($cons->repeat_class eq 'Simple_repeat') {
my $rcon = $cons->name;
$rcon =~ s/\((\S+)\)n/$1/; # get repeat element
$cons->repeat_consensus($rcon);
# Look for matches already stored
my $match = $rca->fetch_by_name_class($cons->name, 'Simple_repeat');
if ($match) {
$cons->dbID($match->dbID());
}
else {
$rca->store($cons);
}
} else {
# for other repeats - need to see if a consensus is stored already
if(!$cons->dbID) {
my $match = ($rca->fetch_by_name($cons->name));
if($match) {
#set the consensus dbID to be the same as the database one
$cons->dbID($match->dbID());
} else {
# if we don't match a consensus already stored create a fake one
# and set consensus to 'N' as null seq not allowed
# FIXME: not happy with this, but ho hum ...
warning("Can't find " . $cons->name . "\n");
$cons->repeat_consensus("N");
$rca->store($cons);
}
}
#if (@match > 1) {
#multiple consensi were matched
# $self->warn(@match . " consensi for " . $cons->name . "\n");
#}
}
my $slice = $rf->slice();
if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
throw("RepeatFeature cannot be stored without an associated slice.");
}
my $original = $rf;
my $seq_region_id;
($rf, $seq_region_id) = $self->_pre_store($rf);
$sth->bind_param(1,$seq_region_id,SQL_INTEGER);
$sth->bind_param(2,$rf->start,SQL_INTEGER);
$sth->bind_param(3,$rf->end,SQL_INTEGER);
$sth->bind_param(4,$rf->strand,SQL_TINYINT);
$sth->bind_param(5,$rf->repeat_consensus->dbID,SQL_INTEGER);
$sth->bind_param(6,$rf->hstart,SQL_INTEGER);
$sth->bind_param(7,$rf->hend,SQL_INTEGER);
$sth->bind_param(8,$rf->score,SQL_DOUBLE);
$sth->bind_param(9,$rf->analysis->dbID,SQL_INTEGER);
$sth->execute();
my $db_id = $sth->{'mysql_insertid'}
or throw("Didn't get an insertid from the INSERT statement");
$original->dbID($db_id);
$original->adaptor($self);
}
}
=head2 list_dbIDs
Arg [1] : none
Example : @feature_ids = @{$repeat_feature_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all repeat features in the current db
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : list of ints
Exceptions : none
Caller : ?
Status : Stable
=cut
sub list_dbIDs {
my ($self, $ordered) = @_;
return $self->_list_dbIDs("repeat_feature", undef, $ordered);
}
1;
]]>