From 260001a7dc60ef5e3aa4d18ba3f9903a7ce7c86f Mon Sep 17 00:00:00 2001
From: Nathan Johnson <njohnson@ebi.ac.uk>
Date: Fri, 13 May 2011 08:52:13 +0000
Subject: [PATCH] added fetch_Iterator_by_Slice_method
---
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 117 +++++++++++++++++-
1 file changed, 116 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index aef74058f8..5ec5323b41 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -151,6 +151,114 @@ sub fetch_all_by_Slice {
}
+
+=head2 fetch_Iterator_by_Slice_method
+
+ Arg [1] : CODE ref of Slice fetch method
+ Arg [2] : ARRAY ref of parameters for Slice fetch method
+ Arg [3] : Optional int: Slice index in parameters array
+ Arg [4] : Optional int: Slice chunk size. Default=500000
+ Example : my $slice_iter = $feature_adaptor->fetch_Iterator_by_Slice_method
+ ($feature_adaptor->can('fetch_all_by_Slice_Arrays'),
+ \@fetch_method_params,
+ 0,#Slice idx
+ #500 #chunk length
+ );
+
+ while(my $feature = $slice_iter->next && defined $feature){
+ #Do something here
+ }
+
+ Description: Creates an Iterator which chunks the query Slice to facilitate
+ large Slice queries which would have previously run out of memory
+ Returntype : Bio::EnsEMBL::Utils::Iterator
+ Exceptions : Throws if mandatory params not valid
+ Caller : general
+ Status : at risk
+
+=cut
+
+sub fetch_Iterator_by_Slice_method{
+ my ($self, $slice_method_ref, $params_ref, $slice_idx, $chunk_size) = @_;
+
+ if(! ( defined $slice_method_ref &&
+ ref($slice_method_ref) eq 'CODE')
+ ){
+ throw('Must pass a valid Slice fetch method CODE ref');
+ }
+
+ if (! ($params_ref &&
+ ref($params_ref) eq 'ARRAY')) {
+ #Don't need to check size here so long as we have valid Slice
+ throw('You must pass a method params ARRAYREF');
+ }
+
+ $slice_idx = 0 if(! defined $slice_idx);
+ my $slice = $params_ref->[$slice_idx];
+ $chunk_size ||= 1000000;
+
+ my @feat_cache;
+ my $finished = 0;
+ my $start = 1; #local coord for sub slice
+ my $end = $slice->length;
+ my $num_overlaps = 0;
+
+ my $coderef =
+ sub {
+
+ while (scalar(@feat_cache) == 0 &&
+ ! $finished) {
+
+ my $new_end = $start + $chunk_size;
+
+ if ($new_end >= $end) {
+ # this is our last chunk
+ $new_end = $end;
+ $finished = 1;
+ }
+
+ #Chunk by sub slicing
+ my $sub_slice = $slice->sub_Slice($start, $new_end);
+ $params_ref->[$slice_idx] = $sub_slice;
+ @feat_cache = @{ $slice_method_ref->($self, @$params_ref)};
+
+
+ #Remove & count overlapping features
+ splice(@feat_cache, 0, $num_overlaps) if($num_overlaps);
+ my $i;
+
+ if (scalar(@feat_cache) > 0) {
+
+ my $feat_end = $feat_cache[$#feat_cache]->end;
+ my $slice_end = $sub_slice->end;
+ $num_overlaps = 0;
+
+ for ($i = $#feat_cache; $i >=0; $i--) {
+
+ if ($feat_end > $slice_end) {
+ $feat_end = $feat_cache[$i]->end;
+ $num_overlaps ++;
+ } else {
+ last;
+ }
+
+ }
+ }
+
+ # update the start coordinate
+ $start = $new_end + 1;
+ }
+
+ #this maybe returning from an undef cache
+ #Need to sub this out even more?
+
+ return shift @feat_cache;
+ };
+
+ return Bio::EnsEMBL::Utils::Iterator->new($coderef);
+}
+
+
=head2 fetch_all_by_Slice_and_score
Arg [1] : Bio::EnsEMBL::Slice $slice
@@ -216,6 +324,7 @@ sub fetch_all_by_Slice_and_score {
sub fetch_all_by_Slice_constraint {
my ( $self, $slice, $constraint, $logic_name ) = @_;
+
my @result = ();
if ( !ref($slice)
@@ -275,6 +384,8 @@ sub fetch_all_by_Slice_constraint {
# Hap/PAR support: retrieve normalized 'non-symlinked' slices.
my @proj = @{ $sa->fetch_normalized_slice_projection($slice) };
+
+
if ( !@proj ) {
throw( 'Could not retrieve normalized Slices. '
. 'Database contains incorrect assembly_exception information.'
@@ -309,12 +420,15 @@ sub fetch_all_by_Slice_constraint {
@bounds = map { $_->from_start() - $slice->start() + 1 } @ent_proj;
+
# fetch features for the primary slice AND all symlinked slices
foreach my $seg (@proj) {
+
+
my $offset = $seg->from_start();
my $seg_slice = $seg->to_Slice();
my $features =
- $self->_slice_fetch( $seg_slice, $constraint ); ## NO RESULTS
+ $self->_slice_fetch( $seg_slice, $constraint );
# If this was a symlinked slice offset the feature coordinates as
# needed.
@@ -492,6 +606,7 @@ sub _slice_fetch {
" AND ${tab_syn}.seq_region_start >= $min_start";
}
+
my $fs = $self->generic_fetch($constraint,undef,$slice);
# features may still have to have coordinates made relative to slice
--
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