From cc819fca21cc3b074e472e738d56f76a847207de Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Tue, 7 Aug 2012 14:48:34 +0000
Subject: [PATCH] added early exit conditions : - if more than max_run
iterations - if all features have been found
run on blocks only if slice is part of the karyotype
run on full slice else
---
.../Pipeline/Production/DensityGenerator.pm | 45 ++++++++++++++-----
1 file changed, 35 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm b/modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm
index f71a027889..19a7229e2a 100644
--- a/modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm
+++ b/modules/Bio/EnsEMBL/Pipeline/Production/DensityGenerator.pm
@@ -21,6 +21,7 @@ sub run {
my $helper = $dba->dbc()->sql_helper();
my $dfa = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'DensityFeature');
my $analysis = $self->get_analysis($logic_name);
+ my $max_run = $self->param('max_run');
$self->delete_old_features($dba, $logic_name);
$self->check_analysis($dba);
@@ -28,24 +29,44 @@ sub run {
my $density_type = $self->get_density_type($analysis);
Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'DensityType')->store($density_type);
my $slices = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'slice')->fetch_all('toplevel');
+ my $option = $self->get_option();
+ my $total = $self->get_total($option);
+ my $count = 0;
+ my @features;
+ my $iteration = 0;
my @sorted_slices =
sort( { $a->coord_system()->rank() <=> $b->coord_system()->rank()
|| $b->seq_region_length() <=> $a->seq_region_length() } @$slices) ;
while (my $slice = shift @sorted_slices) {
- my @blocks = $self->generate_blocks($slice);
- foreach my $block (@blocks) {
- my $feature = $self->get_density($block, $slice);
+ $iteration++;
+ if ($slice->has_karyotype) {
+ my @blocks = $self->generate_blocks($slice);
+ for my $block (@blocks) {
+ my $feature = $self->get_density($block, $option);
+ $count += $feature;
+ my $df = Bio::EnsEMBL::DensityFeature->new( -seq_region => $slice,
+ -start => $block->start,
+ -end => $block->end,
+ -density_type => $density_type,
+ -density_value => $feature);
+ push(@features, $df);
+ }
+ } else {
+ my $feature = $self->get_density($slice, $option);
+ $count += $feature;
my $df = Bio::EnsEMBL::DensityFeature->new( -seq_region => $slice,
- -start => $block->start,
- -end => $block->end,
+ -start => $slice->start,
+ -end => $slice->end,
-density_type => $density_type,
-density_value => $feature);
- if ($feature > 0) {
- $dfa->store($df);
- }
+ push(@features, $df);
+ }
+ if ($count >= $total || $iteration > $max_run) {
+ last;
}
}
+ $dfa->store(@features);
}
@@ -163,7 +184,7 @@ sub get_analysis {
}
sub get_biotype_group {
- my ($self, $biotype) = @_;
+ my ($self, $group) = @_;
my $prod_dba = $self->get_production_DBAdaptor();
my $helper = $prod_dba->dbc()->sql_helper();
my $sql = q{
@@ -173,9 +194,13 @@ sub get_biotype_group {
AND is_current = 1
AND biotype_group = ?
AND db_type like '%core%' };
- my @biotypes = @{ $helper->execute_simple(-SQL => $sql, -PARAMS => [$biotype]) };
+ my @biotypes = @{ $helper->execute_simple(-SQL => $sql, -PARAMS => [$group]) };
return @biotypes;
}
+sub get_option {
+ my $self = @_;
+}
+
1;
--
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