From 5cd7ec3bd2cf8d76042f080bf69035db2e7ea3ec Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 11 Apr 2012 17:08:56 +0000
Subject: [PATCH] store density features in batch
---
misc-scripts/density_feature/variation_density.pl | 12 ++++++++----
1 file changed, 8 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/density_feature/variation_density.pl b/misc-scripts/density_feature/variation_density.pl
index 846db569ad..d7dc86b60c 100644
--- a/misc-scripts/density_feature/variation_density.pl
+++ b/misc-scripts/density_feature/variation_density.pl
@@ -115,6 +115,8 @@ while ( my $slice = shift @sorted_slices){
$block_size = $slice->length() / $bin_count;
+ my @density_features;
+
print STDOUT "Calculating SNP densities for ". $slice->seq_region_name() . " with block size $block_size\n";
$current_end = 0;
@@ -138,18 +140,20 @@ while ( my $slice = shift @sorted_slices){
$sth->execute($slice->get_seq_region_id(), $current_end, $current_start);
my $count = ($sth->fetchrow_array())[0];
- my $df = Bio::EnsEMBL::DensityFeature->new(-seq_region => $slice,
+ push @density_features, Bio::EnsEMBL::DensityFeature->new(-seq_region => $slice,
-start => $current_start,
-end => $current_end,
-density_type => $dt,
-density_value => $count);
- $density_feature_adaptor->store($df);
- if ($df->dbID()) {
- $total_count ++;
+ if ($count > 0) {
+ #density features with value = 0 are not stored
+ $total_count++;
}
}
+ $density_feature_adaptor->store(@density_features);
+
last if ( $slice_count++ > $max_slices );
}
--
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