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Commit c4a5cddc authored by Graham McVicker's avatar Graham McVicker
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tidied and split large fetch_all_by_Slice_constraint method into 2 smaller methods

parent 20789164
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modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
View file @ c4a5cddc
......@@ -40,8 +40,8 @@ use Bio::EnsEMBL::Utils::Argument qw(rearrange);
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
my $SLICE_FEATURE_CACHE_SIZE = 4;
my $MAX_SPLIT_QUERY_SEQ_REGIONS = 3;
our $SLICE_FEATURE_CACHE_SIZE = 4;
our $MAX_SPLIT_QUERY_SEQ_REGIONS = 3;
=head2 new
......@@ -72,19 +72,17 @@ sub new {
=head2 _straight_join
# _straight_join
Arg [1] : (optional) boolean $new_val
Example : $self->_straight_join(1);
$self->generic_fetch($constraint);
$self->_straight_join(0);
Description: Getter/Setter that turns on/off the use of a straight join
in queries.
Returntype : boolean
Exceptions : none
Caller : general
=cut
# Arg [1] : (optional) boolean $new_val
# Example : $self->_straight_join(1);
# $self->generic_fetch($constraint);
# $self->_straight_join(0);
# Description: PROTECTED Getter/Setter that turns on/off the use of
# a straight join in queries.
# Returntype : boolean
# Exceptions : none
# Caller : general
sub _straight_join {
my $self = shift;
......@@ -255,8 +253,8 @@ sub fetch_all_by_dbID_list {
my @tabs = $self->_tables;
my ($name, $syn) = @{$tabs[0]};
#mysql is faster and we ensure that we do not exceed the max query size by
#splitting large queries into smaller queries of 200 ids
# mysql is faster and we ensure that we do not exceed the max query size by
# splitting large queries into smaller queries of 200 ids
my $max_size = 200;
while(@$id_list) {
......@@ -267,7 +265,6 @@ sub fetch_all_by_dbID_list {
@ids = splice(@$id_list, 0);
}
my $id_str;
if(@ids > 1) {
$id_str = " IN (" . join(',', @ids). ")";
......@@ -366,175 +363,184 @@ sub fetch_all_by_Slice_and_score {
=cut
sub fetch_all_by_Slice_constraint {
my($self, $orig_slice, $original_constraint, $logic_name) = @_;
my @result_features;
my($self, $slice, $constraint, $logic_name) = @_;
my @result;
if(!ref($orig_slice) || !$orig_slice->isa("Bio::EnsEMBL::Slice")) {
if(!ref($slice) || !$slice->isa("Bio::EnsEMBL::Slice")) {
throw("Bio::EnsEMBL::Slice argument expected.");
}
$original_constraint ||= '';
$original_constraint = $self->_logic_name_to_constraint($original_constraint,
$logic_name);
$constraint ||= '';
$constraint = $self->_logic_name_to_constraint($constraint, $logic_name);
#if the logic name was invalid, undef was returned
return [] if(!defined($original_constraint));
return [] if(!defined($constraint));
#check the cache and return if we have already done this query
my $key = uc(join(':', $orig_slice->name, $original_constraint));
my $key = uc(join(':', $slice->name, $constraint));
if(exists($self->{'_slice_feature_cache'}->{$key})) {
return $self->{'_slice_feature_cache'}->{$key};
}
my $slice_adaptor = $orig_slice->adaptor();
my $sa = $slice->adaptor();
#retrieve normalized 'non-symlinked' slices
#this allows us to support haplotypes and PARs
my @projection =
@{$slice_adaptor->fetch_normalized_slice_projection($orig_slice)};
# Hap/PAR support: retrieve normalized 'non-symlinked' slices
my @proj = @{$sa->fetch_normalized_slice_projection($slice)};
if(@projection == 0) {
if(@proj == 0) {
throw('Could not retrieve normalized Slices. Database contains ' .
'incorrect assembly_exception information.');
}
#we want to retrieve all features calculated on the FULL original slice
#as well as any symlinked slices.
# Want to get features on the FULL original slice
# as well as any symlinked slices
#Filter out any partial slices from the normalized projection that are on
#the same seq region as the original slice
my @new_projection =
grep { $_->[2]->seq_region_name() ne $orig_slice->seq_region_name() }
@projection;
# Filter out partial slices from projection that are on
# same seq_region as original slice
push( @new_projection, [ 1, $orig_slice->length(), $orig_slice ] );
my $sr_id = $slice->get_seq_region_id();
#fetch features for the primary slice AND all symlinked slices
foreach my $segment (@new_projection) {
my ($offset, $slice);
($offset, undef, $slice) = @$segment;
@proj = grep { $_->to_Slice->get_seq_region_id() != $sr_id } @proj;
my $slice_start = $slice->start();
my $slice_end = $slice->end();
my $slice_strand = $slice->strand();
my $slice_cs = $slice->coord_system();
my $slice_seq_region = $slice->seq_region_name();
my $segment = bless([1,$slice->length(),$slice ],
'Bio::EnsEMBL::ProjectionSegment');
push( @proj, $segment );
#get the synonym and name of the primary_table
my @tabs = $self->_tables;
my ($tab_name, $tab_syn) = @{$tabs[0]};
# fetch features for the primary slice AND all symlinked slices
foreach my $segment (@proj) {
my $offset = $segment->from_start();
my $seg_slice = $segment->to_Slice();
#find out what coordinate systems the features are in
my $mcc = $self->db->get_MetaCoordContainer();
my @feat_css = @{$mcc->fetch_all_CoordSystems_by_feature_type($tab_name)};
my $features = $self->_slice_fetch($seg_slice, $constraint);
my $asma = $self->db->get_AssemblyMapperAdaptor();
my @features;
# if this was a symlinked slice offset the feature coordinates as needed
if($seg_slice->name() ne $slice->name()) {
foreach my $f (@$features) {
if($offset != 1) {
$f->{'start'} += $offset-1;
$f->{'end'} += $offset-1;
}
$f->{'slice'} = $slice;
push @result, $f;
}
} else {
push @result, @$features;
}
}
$self->{'_slice_feature_cache'}->{$key} = \@result;
# fetch the features from each coordinate system they are stored in
COORD_SYSTEM: foreach my $feat_cs (@feat_css) {
my $mapper;
my @coords;
my @ids;
return \@result;
}
if($feat_cs->equals($slice_cs)) {
#no mapping is required if this is the same coord system
my $constraint = $original_constraint;
# obtain seq_region_id of this slice from db
my $seq_region_id =
$self->db->get_SliceAdaptor->get_seq_region_id($slice);
$constraint .= " AND " if($constraint);
$constraint .=
"${tab_syn}.seq_region_id = $seq_region_id AND " .
#
# helper function used by fetch_all_by_Slice_constraint method
#
sub _slice_fetch {
my $self = shift;
my $slice = shift;
my $orig_constraint = shift;
my $slice_start = $slice->start();
my $slice_end = $slice->end();
my $slice_strand = $slice->strand();
my $slice_cs = $slice->coord_system();
my $slice_seq_region = $slice->seq_region_name();
#get the synonym and name of the primary_table
my @tabs = $self->_tables;
my ($tab_name, $tab_syn) = @{$tabs[0]};
#find out what coordinate systems the features are in
my $mcc = $self->db->get_MetaCoordContainer();
my @feat_css = @{$mcc->fetch_all_CoordSystems_by_feature_type($tab_name)};
my $asma = $self->db->get_AssemblyMapperAdaptor();
my @features;
# fetch the features from each coordinate system they are stored in
COORD_SYSTEM: foreach my $feat_cs (@feat_css) {
my $mapper;
my @coords;
my @ids;
if($feat_cs->equals($slice_cs)) {
# no mapping is required if this is the same coord system
my $constraint = $orig_constraint;
my $sr_id = $self->db->get_SliceAdaptor->get_seq_region_id($slice);
$constraint .= " AND " if($constraint);
$constraint .=
"${tab_syn}.seq_region_id = $sr_id AND " .
"${tab_syn}.seq_region_start <= $slice_end AND " .
"${tab_syn}.seq_region_end >= $slice_start";
my $fs = $self->generic_fetch($constraint,undef,$slice);
my $fs = $self->generic_fetch($constraint,undef,$slice);
#features may still have to have coordinates made relative to slice
#start
$fs = $self->_remap($fs, $mapper, $slice);
# features may still have to have coordinates made relative to slice
# start
$fs = $self->_remap($fs, $mapper, $slice);
push @features, @$fs;
} else {
$mapper = $asma->fetch_by_CoordSystems($slice_cs, $feat_cs);
# Get a list of coordinates and corresponding internal ids for the
# regions we are interested in
@coords = $mapper->map($slice_seq_region, $slice_start, $slice_end,
$slice_strand, $slice_cs);
@coords = grep {!$_->isa('Bio::EnsEMBL::Mapper::Gap')} @coords;
next COORD_SYSTEM if(!@coords);
@ids = map {$_->id()} @coords;
@ids = @{$asma->seq_regions_to_ids($feat_cs, \@ids)};
#if the regions are large and only partially spanned
#it is faster to to limit the query with start and end constraints
#however, it is difficult to tell if a region is large and only
#partially wanted. The easy approach is just to limit the queries if
#there are less than a certain number of regions. As well seperate
#queries are needed otherwise the indices will not be useful
if(@coords > $MAX_SPLIT_QUERY_SEQ_REGIONS) {
#do one query, and do not limit with start / end constraints
my $constraint = $original_constraint;
my $id_str = join(',', @ids);
$constraint .= " AND " if($constraint);
$constraint .= "${tab_syn}.seq_region_id IN ($id_str)";
push @features, @$fs;
} else {
$mapper = $asma->fetch_by_CoordSystems($slice_cs, $feat_cs);
my $fs =
$self->generic_fetch($constraint, $mapper, $slice);
# Get list of coordinates and corresponding internal ids for
# regions the slice spans
@coords = $mapper->map($slice_seq_region, $slice_start, $slice_end,
$slice_strand, $slice_cs);
$fs = $self->_remap($fs, $mapper, $slice);
@coords = grep {!$_->isa('Bio::EnsEMBL::Mapper::Gap')} @coords;
push @features, @$fs;
next COORD_SYSTEM if(!@coords);
@ids = map {$_->id()} @coords;
@ids = @{$asma->seq_regions_to_ids($feat_cs, \@ids)};
# When regions are large and only partially spanned by slice
# it is faster to to limit the query with start and end constraints.
# Take simple approach: use regional constraints if there are less
# than a specific number of regions covered.
if(@coords > $MAX_SPLIT_QUERY_SEQ_REGIONS) {
my $constraint = $orig_constraint;
my $id_str = join(',', @ids);
$constraint .= " AND " if($constraint);
$constraint .= "${tab_syn}.seq_region_id IN ($id_str)";
my $fs = $self->generic_fetch($constraint, $mapper, $slice);
} else {
#do multiple split queries using start / end constraints
my $len = @coords;
for(my $i = 0; $i < $len; $i++) {
my $constraint = $original_constraint;
$constraint .= " AND " if($constraint);
$constraint .=
$fs = $self->_remap($fs, $mapper, $slice);
push @features, @$fs;
} else {
# do multiple split queries using start / end constraints
my $len = @coords;
for(my $i = 0; $i < $len; $i++) {
my $constraint = $orig_constraint;
$constraint .= " AND " if($constraint);
$constraint .=
"${tab_syn}.seq_region_id = " . $ids[$i] . " AND " .
"${tab_syn}.seq_region_start <= " . $coords[$i]->end() . " AND ".
"${tab_syn}.seq_region_end >= " . $coords[$i]->start();
my $fs = $self->generic_fetch($constraint,$mapper,$slice);
my $fs = $self->generic_fetch($constraint,$mapper,$slice);
$fs = $self->_remap($fs, $mapper, $slice);
push @features, @$fs;
}
}
}
} #COORD system loop
$fs = $self->_remap($fs, $mapper, $slice);
#if this was a symlinked slice offset the feature coordinates as needed
if($slice != $orig_slice) {
foreach my $f (@features) {
#function calls are slow!
if($offset != 1) {
$f->{'start'} += $offset-1;
$f->{'end'} += $offset-1;
push @features, @$fs;
}
$f->{'slice'} = $orig_slice;
push @result_features, $f;
}
} else {
push @result_features, @features;
}
} #COORD system loop
} #slice & symmlinked slice loop
$self->{'_slice_feature_cache'}->{$key} = \@result_features;
return \@result_features;
return \@features;
}
#
# Helper function containing some common feature storing functionality
#
......@@ -568,10 +574,9 @@ sub _pre_store {
throw('Feature must be attached to Slice to be stored.');
}
# make sure that the feature coordinates are relative to
# the start of the entire seq_region
# make sure feature coords are relative to start of entire seq_region
if($slice->start != 1 || $slice->strand != 1) {
#move the feature onto a slice of the entire seq_region
#move feature onto a slice of the entire seq_region
$slice = $slice_adaptor->fetch_by_region($slice->coord_system->name(),
$slice->seq_region_name(),
undef, #start
......@@ -587,10 +592,7 @@ sub _pre_store {
}
}
#
# Ensure that this type of feature is known to be stored in this coord
# system.
#
# Ensure this type of feature is known to be stored in this coord system.
my $cs = $slice->coord_system;
my ($tab) = $self->_tables();
......@@ -600,23 +602,6 @@ sub _pre_store {
$mcc->add_feature_type($cs, $tabname);
# we have to update the meta coord table in both the dna db and the feature
# db so that the feature db can be used independently later
# Actually, the meta coord info should probably only go in the database
# where the features are actually stored, not the dnadb (which is often
# going to be read-only anyway)
# if($db->dnadb() != $db) {
# my $dnadb = $db->dnadb();
# $db->dnadb(undef); # unset the dnadb temporarily
# #get a coord system adaptor from the feature database
# $csa = $db->get_CoordSystemAdaptor();
# $csa->add_feature_table($cs, $tabname);
# $db->dnadb($dnadb); # reinstate the dnadb
# }
my $seq_region_id = $slice_adaptor->get_seq_region_id($slice);
if(!$seq_region_id) {
......@@ -767,8 +752,6 @@ sub _logic_name_to_constraint {
my $an = $aa->fetch_by_logic_name($logic_name);
if(!$an) {
warning("No analysis exists with logic_name = [$logic_name].\n" .
"Returning empty list.\n");
return undef;
}
......
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