Raw content of Bio::EnsEMBL::DBSQL::OligoFeatureAdaptor
<![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::OligoFeatureAdaptor - A database adaptor for fetching and
storing OligoFeature objects.
=head1 SYNOPSIS
my $ofa = $db->get_OligoFeatureAdaptor();
my $features = $ofa->fetch_all_by_Probe($probe);
$features =
$ofa->fetch_all_by_Slice_arrayname( $slice, 'Array-1', 'Array-2' );
=head1 DESCRIPTION
The OligoFeatureAdaptor is a database adaptor for storing and retrieving
OligoFeature objects.
=head1 METHODS
=cut
package Bio::EnsEMBL::DBSQL::OligoFeatureAdaptor;
use strict;
use warnings;
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
use Bio::EnsEMBL::OligoFeature;
use Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor);
=head2 fetch_all_by_Probe
Arg [1] : Bio::EnsEMBL::OligoProbe
Example : my $features = $ofa->fetch_all_by_Probe($probe);
Description: Fetchs all features that a given probe creates.
Returntype : Listref of Bio::EnsEMBL::OligoFeature objects
Exceptions : Throws if argument is not a stored OligoProbe object
Caller : OligoProbe->get_all_OligoFeatures()
Status : Medium Risk
=cut
sub fetch_all_by_Probe {
my $self = shift;
my $probe = shift;
if ( !ref($probe) && !$probe->isa('Bio::EnsEMBL::OligoProbe') ) {
throw('fetch_all_by_Probe requires a Bio::EnsEMBL::OligoProbe object');
}
if ( !defined $probe->dbID() ) {
throw('fetch_all_by_Probe requires a stored Bio::EnsEMBL::OligoProbe object');
}
$self->bind_param_generic_fetch($probe->dbID(),SQL_INTEGER);
return $self->generic_fetch( 'of.oligo_probe_id = ?' );
}
=head2 fetch_all_by_probeset
Arg [1] : string - probeset
Example : my $features = $ofa->fetch_all_by_probeset('Set-1');
Description: Fetchs all features that a given probeset creates.
Returntype : Listref of Bio::EnsEMBL::OligoFeature objects
Exceptions : Throws if no probeset argument
Caller : General
Status : Medium Risk
=cut
sub fetch_all_by_probeset {
my $self = shift;
my $probeset = shift;
if (!$probeset) {
throw('fetch_all_by_probeset requires a probeset argument');
}
$self->bind_param_generic_fetch($probeset,SQL_VARCHAR);
return $self->generic_fetch( "op.probeset = ?" );
}
=head2 fetch_all_by_Slice_arrayname
Arg [1] : Bio::EnsEMBL::Slice
Arg [2...] : List of strings - array name(s)
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $ofa->fetch_by_Slice_arrayname($slice, '');
Description: Retrieves a list of features on a given slice that are created
by probes from the specified arrays.
Returntype : Listref of Bio::EnsEMBL::OligoFeature objects
Exceptions : Throws if no array name is provided
Caller : Slice->get_all_OligoFeatures()
Status : Medium Risk
=cut
sub fetch_all_by_Slice_arrayname {
my ($self, $slice, @arraynames) = @_;
throw('Need array name as parameter') if !@arraynames;
my $constraint;
if (scalar @arraynames == 1) {
$constraint = qq( oa.name = '$arraynames[0]' );
} else {
$constraint = join q(','), @arraynames;
$constraint = qq( oa.name IN ('$constraint') );
}
return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint);
}
=head2 fetch_all_by_Slice_type
Arg [1] : Bio::EnsEMBL::Slice
Arg [2] : string - type of array (e.g. AFFY or OLIGO)
Arg [3] : (optional) string - logic name
Example : my $slice = $sa->fetch_by_region('chromosome', '1');
my $features = $ofa->fetch_by_Slice_type($slice, 'OLIGO');
Description: Retrieves a list of features on a given slice that are created
by probes from the specified type of array.
Returntype : Listref of Bio::EnsEMBL::OligoFeature objects
Exceptions : Throws if no array type is provided
Caller : General
Status : Medium Risk
=cut
sub fetch_all_by_Slice_type {
my ($self, $slice, $type, $logic_name) = @_;
throw('Need type as parameter') if !$type;
my $constraint = qq( oa.type = '$type' );
return $self->SUPER::fetch_all_by_Slice_constraint($slice, $constraint, $logic_name);
}
=head2 _tables
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns the names and aliases of the tables to use for queries.
Returntype : List of listrefs of strings
Exceptions : None
Caller : Internal
Status : Medium Risk
=cut
sub _tables {
my $self = shift;
return (
[ 'oligo_feature', 'of' ],
[ 'oligo_probe', 'op' ],
[ 'oligo_array', 'oa' ]
);
}
=head2 _columns
Args : 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
Status : Medium Risk
=cut
sub _columns {
my $self = shift;
return qw(
of.oligo_feature_id of.seq_region_id
of.seq_region_start of.seq_region_end
of.seq_region_strand of.mismatches
of.oligo_probe_id of.analysis_id
oa.name op.probeset
op.name
);
}
=head2 _default_where_clause
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns an additional table joining constraint to use for
queries.
Returntype : List of strings
Exceptions : None
Caller : Internal
Status : Medium Risk
=cut
sub _default_where_clause {
my $self = shift;
return 'of.oligo_probe_id = op.oligo_probe_id AND op.oligo_array_id = oa.oligo_array_id';
}
=head2 _final_clause
Args : None
Example : None
Description: PROTECTED implementation of superclass abstract method.
Returns an ORDER BY clause. Sorting by oligo_feature_id would be
enough to eliminate duplicates, but sorting by location might
make fetching features on a slice faster.
Returntype : String
Exceptions : None
Caller : generic_fetch
Status : Medium Risk
=cut
sub _final_clause {
return ' ORDER BY of.seq_region_id, of.seq_region_start, of.oligo_feature_id';
}
=head2 _objs_from_sth
Arg [1] : DBI statement handle object
Example : None
Description: PROTECTED implementation of superclass abstract method.
Creates OligoFeature objects from an executed DBI statement
handle.
Returntype : Listref of Bio::EnsEMBL::OligoFeature objects
Exceptions : None
Caller : Internal
Status : Medium Risk
=cut
sub _objs_from_sth {
my ($self, $sth, $mapper, $dest_slice) = @_;
# This code is ugly because caching is used to improve speed
my $sa = $self->db->get_SliceAdaptor();
my $aa = $self->db->get_AnalysisAdaptor();
my @features;
my (%analysis_hash, %slice_hash, %sr_name_hash, %sr_cs_hash);
my (
$oligo_feature_id, $seq_region_id,
$seq_region_start, $seq_region_end,
$seq_region_strand, $mismatches,
$oligo_probe_id, $analysis_id,
$array_name, $probeset,
$oligo_probe_name,
);
$sth->bind_columns(
\$oligo_feature_id, \$seq_region_id,
\$seq_region_start, \$seq_region_end,
\$seq_region_strand, \$mismatches,
\$oligo_probe_id, \$analysis_id,
\$array_name, \$probeset,
\$oligo_probe_name,
);
my $asm_cs;
my $cmp_cs;
my $asm_cs_name;
my $asm_cs_vers;
my $cmp_cs_name;
my $cmp_cs_vers;
if ($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();
}
my $last_feature_id = -1;
FEATURE: while ( $sth->fetch() ) {
# This assumes that features come out sorted by ID
next if ($last_feature_id == $oligo_feature_id);
$last_feature_id = $oligo_feature_id;
# Get the analysis object
my $analysis = $analysis_hash{$analysis_id} ||= $aa->fetch_by_dbID($analysis_id);
# Get the slice object
#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, $asm_cs_vers);
# }
}
# If a destination slice was provided convert the coords
# If the destination slice starts at 1 and is forward strand, nothing needs doing
if ($dest_slice) {
unless ($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
next FEATURE if $seq_region_end < 1 || $seq_region_start > $dest_slice_length
|| ( $dest_slice_sr_id ne $seq_region_id );
$slice = $dest_slice;
}
push @features, $self->_new_fast( {
'start' => $seq_region_start,
'end' => $seq_region_end,
'strand' => $seq_region_strand,
'slice' => $slice,
'analysis' => $analysis,
'adaptor' => $self,
'dbID' => $oligo_feature_id,
'mismatchcount' => $mismatches,
'_probe_id' => $oligo_probe_id,
'probeset' => $probeset,
'_probe_name' => $oligo_probe_name
} );
}
return \@features;
}
=head2 _new_fast
Args : Hashref to be passed to OligoFeature->new_fast()
Example : None
Description: Construct an OligoFeature object using quick and dirty new_fast.
Returntype : Bio::EnsEMBL::OligoFeature
Exceptions : None
Caller : _objs_from_sth
Status : Medium Risk
=cut
sub _new_fast {
my $self = shift;
my $hash_ref = shift;
return Bio::EnsEMBL::OligoFeature->new_fast($hash_ref);
}
=head2 store
Args : List of Bio::EnsEMBL::OligoFeature objects
Example : $ofa->store(@features);
Description: Stores given OligoFeature objects in the database. Should only
be called once per feature because no checks are made for
duplicates. Sets dbID and adaptor on the objects that it stores.
Returntype : None
Exceptions : Throws if a list of OligoFeature objects is not provided or if
an analysis is not attached to any of the objects
Caller : General
Status : Medium Risk
=cut
sub store{
my ($self, @ofs) = @_;
if (scalar(@ofs) == 0) {
throw('Must call store with a list of OligoFeature objects');
}
my $sth = $self->prepare("
INSERT INTO oligo_feature (
seq_region_id, seq_region_start,
seq_region_end, seq_region_strand,
oligo_probe_id, analysis_id,
mismatches
) VALUES (?, ?, ?, ?, ?, ?, ?)
");
my $db = $self->db();
my $analysis_adaptor = $db->get_AnalysisAdaptor();
FEATURE: foreach my $of (@ofs) {
if( !ref $of || !$of->isa('Bio::EnsEMBL::OligoFeature') ) {
throw('Feature must be an OligoFeature object');
}
if ( $of->is_stored($db) ) {
warning('OligoFeature [' . $of->dbID() . '] is already stored in the database');
next FEATURE;
}
if ( !defined $of->analysis() ) {
throw('An analysis must be attached to the OligoFeature objects to be stored.');
}
# Store the analysis if it has not been stored yet
if ( !$of->analysis->is_stored($db) ) {
$analysis_adaptor->store( $of->analysis() );
}
my $original = $of;
my $seq_region_id;
($of, $seq_region_id) = $self->_pre_store($of);
$sth->bind_param(1, $seq_region_id, SQL_INTEGER);
$sth->bind_param(2, $of->start(), SQL_INTEGER);
$sth->bind_param(3, $of->end(), SQL_INTEGER);
$sth->bind_param(4, $of->strand(), SQL_TINYINT);
$sth->bind_param(5, $of->probe->dbID(), SQL_INTEGER);
$sth->bind_param(6, $of->analysis->dbID(), SQL_INTEGER);
$sth->bind_param(7, $of->mismatchcount(), SQL_TINYINT);
$sth->execute();
$original->dbID( $sth->{'mysql_insertid'} );
$original->adaptor($self);
}
}
=head2 list_dbIDs
Args : None
Example : my @feature_ids = @{$ofa->list_dbIDs()};
Description: Gets an array of internal IDs for all OligoFeature objects in
the current database.
Arg[1] : <optional> int. not 0 for the ids to be sorted by the seq_region.
Returntype : List of ints
Exceptions : None
Caller : ?
Status : Medium Risk
=cut
sub list_dbIDs {
my ($self,$ordered) = shift;
return $self->_list_dbIDs('oligo_feature',undef,$ordered);
}
1;
]]>