Commit dfce65c7 authored by Daniel Rios's avatar Daniel Rios
Browse files

added new methods to store/remove AssemblyExceptionFeature objects in the database

parent ef7bccad
......@@ -147,6 +147,7 @@ sub fetch_all {
# each row creates TWO features, each of which has alternate_slice
# pointing to the "other" one
my $a = Bio::EnsEMBL::AssemblyExceptionFeature->new
('-dbID' => $ax_id,
'-start' => $sr_start,
......@@ -156,7 +157,7 @@ sub fetch_all {
'-slice' => $slice,
'-alternate_slice' => $x_slice->sub_Slice($x_sr_start, $x_sr_end),
'-type' => $x_type);
push @features, $a;
$self->{'_aexc_dbID_cache'}->{$ax_id} = $a;
......@@ -344,7 +345,274 @@ sub _remap {
return \@out;
=head2 store
Arg[1] : Bio::EnsEMBL::AssemblyException $asx
Arg[2] : Bio::EnsEMBL::AssemblyException $asx2
Example : $asx = Bio::EnsEMBL::AssemblyExceptionFeature->new(...)
$asx2 = Bio::EnsEMBL::AssemblyExceptionFeature->new(...)
$asx_seq_region_id = $asx_adaptor->store($asx);
Description: This stores a assembly exception feature in the
assembly_exception table and returns the assembly_exception_id.
Needs 2 features: one pointing to the Assembly_exception, and the
other pointing to the region in the reference that is being mapped to
Will check that start, end and type are defined, and the alternate
slice is present as well.
ReturnType: int
Exceptions: throw if assembly exception not defined (needs start, end,
type and alternate_slice) of if $asx not a Bio::EnsEMBL::AssemblyException
Caller: general
Status: Stable
use Data::Dumper;
sub store{
my $self = shift;
my $asx = shift;
my $asx2 = shift;
if (! $asx->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
throw("$asx is not a Ensembl assemlby exception -- not stored");
#if already present, return ID in the database
my $db = $self->db();
if ($asx->is_stored($db)){
return $asx->dbID();
#do some checkings for the object
#at the moment, the orientation is always 1
if (! $asx->start || ! $asx->end ){
throw("Assembly exception does not have coordinates");
if ($asx->type !~ /PAR|HAP/){
throw("Only types of assembly exception features valid are PAR and HAP");
if (! $asx->alternate_slice->isa('Bio::EnsEMBL::Slice')){
throw("Alternate slice should be a Bio::EnsEMBL::Slice");
#now check the other Assembly exception feature, the one pointing to the REF
# region
if (!$asx2->isa('Bio::EnsEMBL::AssemblyExceptionFeature')){
throw("$asx2 is not a Ensembl assemlby exception -- not stored");
if (! $asx2->start || ! $asx2->end ){
throw("Assembly exception does not have coordinates");
if ($asx2->type !~ /HAP REF|PAR REF/){
throw("$asx2 should have type of assembly exception features HAP REF or PAR REF");
if (! $asx->alternate_slice->isa('Bio::EnsEMBL::Slice')){
throw("Alternate slice should be a Bio::EnsEMBL::Slice");
#finally check that both features are pointing to each other slice
if ($asx->slice != $asx2->alternate_slice || $asx->alternate_slice != $asx2->slice){
throw("Slice and alternate slice in both features are not pointing to each other");
#prepare the SQL
my $asx_sql = q{
INSERT INTO assembly_exception( seq_region_id, seq_region_start,
exc_type, exc_seq_region_id,
exc_seq_region_start, exc_seq_region_end,
VALUES (?, ?, ?, ?, ?, ?, ?, 1)
my $asx_st = $self->prepare($asx_sql);
my $asx_id = undef;
my $asx_seq_region_id;
my $asx2_seq_region_id;
my $original = $asx;
my $original2 = $asx2;
#check all feature information
($asx, $asx_seq_region_id) = $self->_pre_store($asx);
($asx2, $asx2_seq_region_id) = $self->_pre_store($asx2);
#and store it
$asx_st->bind_param(1, $asx_seq_region_id, SQL_INTEGER);
$asx_st->bind_param(2, $asx->start(), SQL_INTEGER);
$asx_st->bind_param(3, $asx->end(), SQL_INTEGER);
$asx_st->bind_param(4, $asx->type(), SQL_VARCHAR);
$asx_st->bind_param(5, $asx2_seq_region_id, SQL_INTEGER);
$asx_st->bind_param(6, $asx2->start(), SQL_INTEGER);
$asx_st->bind_param(7, $asx2->end(), SQL_INTEGER);
$asx_id = $asx_st->{'mysql_insertid'};
#finally, update the dbID and adaptor of the asx and asx2
#and finally update dbID cache with new assembly exception
$self->{'_aexc_dbID_cache'}->{$asx_id} = $original;
#and update the other caches as well
push @{$self->{'_aexc_slice_cache'}->{uc($asx->slice->name)}},$original, $original2;
push @{$self->{'_aexc_cache'}}, $original, $original2;
return $asx_id;
# Helper function containing some common feature storing functionality
# Given a Feature this will return a copy (or the same feature if no changes
# to the feature are needed) of the feature which is relative to the start
# of the seq_region it is on. The seq_region_id of the seq_region it is on
# is also returned.
# This method will also ensure that the database knows which coordinate
# systems that this feature is stored in.
# Since this adaptor doesn't inherit from BaseFeatureAdaptor, we need to copy
# the code
sub _pre_store {
my $self = shift;
my $feature = shift;
if(!ref($feature) || !$feature->isa('Bio::EnsEMBL::Feature')) {
throw('Expected Feature argument.');
my $db = $self->db();
my $slice_adaptor = $db->get_SliceAdaptor();
my $slice = $feature->slice();
if(!ref($slice) || !$slice->isa('Bio::EnsEMBL::Slice')) {
throw('Feature must be attached to Slice to be stored.');
# make sure feature coords are relative to start of entire seq_region
if($slice->start != 1 || $slice->strand != 1) {
#move feature onto a slice of the entire seq_region
$slice = $slice_adaptor->fetch_by_region($slice->coord_system->name(),
undef, #start
undef, #end
undef, #strand
$feature = $feature->transfer($slice);
if(!$feature) {
throw('Could not transfer Feature to slice of ' .
'entire seq_region prior to storing');
# Ensure this type of feature is known to be stored in this coord system.
my $cs = $slice->coord_system;
my $mcc = $db->get_MetaCoordContainer();
$mcc->add_feature_type($cs, 'assembly_exception', $feature->length);
my $seq_region_id = $slice_adaptor->get_seq_region_id($slice);
if(!$seq_region_id) {
throw('Feature is associated with seq_region which is not in this DB.');
return ($feature, $seq_region_id);
# helper function used to validate start/end/strand and
# hstart/hend/hstrand etc.
sub _check_start_end_strand {
my $self = shift;
my $start = shift;
my $end = shift;
my $strand = shift;
# Make sure that the start, end, strand are valid
if(int($start) != $start) {
throw("Invalid Feature start [$start]. Must be integer.");
if(int($end) != $end) {
throw("Invalid Feature end [$end]. Must be integer.");
if(int($strand) != $strand || $strand < -1 || $strand > 1) {
throw("Invalid Feature strand [$strand]. Must be -1, 0 or 1.");
if($end < $start) {
throw("Invalid Feature start/end [$start/$end]. Start must be less " .
"than or equal to end.");
return 1;
=head2 remove
Arg [1] : $asx Bio::EnsEMBL::AssemblyFeatureException
Example : $asx_adaptor->remove($asx);
Description: This removes a assembly exception feature from the database.
Returntype : none
Exceptions : thrown if $asx arg does not implement dbID(), or if
$asx->dbID is not a true value
Caller : general
Status : Stable
#again, this method is generic in BaseFeatureAdaptor, but since this class
#is not inheriting, need to copy&paste
sub remove {
my ($self, $feature) = @_;
if(!$feature || !ref($feature) || !$feature->isa('Bio::EnsEMBL::AssemblyExceptionFeature')) {
throw('AssemblyExceptionFeature argument is required');
if(!$feature->is_stored($self->db)) {
throw("This feature is not stored in this database");
my $asx_id = $feature->dbID();
my $key = uc($feature->slice->name);
my $sth = $self->prepare("DELETE FROM assembly_exception WHERE assembly_exception_id = ?");
#and clear cache
#and finally update dbID cache
delete $self->{'_aexc_dbID_cache'}->{$asx_id};
#and remove from cache feature
my @features;
foreach my $asx (@{$self->{'_aexc_slice_cache'}->{$key}}){
if ($asx->dbID != $asx_id){
push @features, $asx;
$self->{'_aexc_slice_cache'}->{$key} = \@features;
@features = ();
foreach my $asx (@{$self->{'_aexc_cache'}}){
if ($asx->dbID != $asx_id){
push @features, $asx;
$self->{'_aexc_cache'} = \@features;
#unset the feature dbID ad adaptor
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