From 878bbdcea977178288b6d73ce874354fd4203ab3 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Fri, 21 May 2004 15:11:12 +0000
Subject: [PATCH] store each density feature as it is created rather than
building a list per seq_region - smaller memory footprint (but repeats still
leaking mem)
---
.../density_feature/percent_gc_calc.pl | 24 +++++--------
.../density_feature/repeat_coverage_calc.pl | 36 ++++++++-----------
.../density_feature/snp_lite_density.pl | 11 ++----
3 files changed, 26 insertions(+), 45 deletions(-)
diff --git a/misc-scripts/density_feature/percent_gc_calc.pl b/misc-scripts/density_feature/percent_gc_calc.pl
index a92980555d..1e5bb90adc 100644
--- a/misc-scripts/density_feature/percent_gc_calc.pl
+++ b/misc-scripts/density_feature/percent_gc_calc.pl
@@ -115,32 +115,26 @@ foreach my $slice ( @$slices ) {
my $blocksize = $density_type->block_size();
$current_start = 1;
- my @density_features=();
-
while($current_start <= $slice->end()) {
$current_end = $current_start+$blocksize-1;
if( $current_end > $slice->end() ) {
- $current_end = $slice->end();
+ $current_end = $slice->end();
}
my $sub_slice = $slice->sub_Slice( $current_start, $current_end );
my $gc = $sub_slice->get_base_count()->{'%gc'};
- push @density_features, Bio::EnsEMBL::DensityFeature->new
- (-seq_region => $slice,
- -start => $current_start,
- -end => $current_end,
- -density_type => $density_type,
- -density_value => $gc);
+ my $df = Bio::EnsEMBL::DensityFeature->new
+ (-seq_region => $slice,
+ -start => $current_start,
+ -end => $current_end,
+ -density_type => $density_type,
+ -density_value => $gc);
+
+ $dfa->store($df);
$current_start = $current_end+1;
}
-
- $dfa->store(@density_features);
- print "Created ",scalar @density_features, " %GC density features ";
- print "for seq_region ", $slice->seq_region_name(),"\n";
-
- # print_features(\@density_features);
}
}
diff --git a/misc-scripts/density_feature/repeat_coverage_calc.pl b/misc-scripts/density_feature/repeat_coverage_calc.pl
index 709b0e407d..32eae04324 100644
--- a/misc-scripts/density_feature/repeat_coverage_calc.pl
+++ b/misc-scripts/density_feature/repeat_coverage_calc.pl
@@ -107,12 +107,10 @@ foreach my $slice ( @$slices ) {
my $blocksize = $density_type->block_size();
$current_start = 1;
- my @density_features=();
-
while($current_start <= $slice->end()) {
$current_end = $current_start+$blocksize-1;
if( $current_end > $slice->end() ) {
- $current_end = $slice->end();
+ $current_end = $slice->end();
}
my $this_block_size = $current_end - $current_start + 1;
@@ -122,35 +120,29 @@ foreach my $slice ( @$slices ) {
my $rr = Bio::EnsEMBL::Mapper::RangeRegistry->new();
foreach my $repeat (@{$sub_slice->get_all_RepeatFeatures()}){
- $rr->check_and_register("1",$repeat->start,$repeat->end);
+ $rr->check_and_register("1",$repeat->start,$repeat->end);
}
my $count = 0;
my $non_repeats = $rr->check_and_register("1",1,$this_block_size);
if( defined $non_repeats ) {
- foreach my $non_repeat ( @$non_repeats ) {
- $count += ($non_repeat->[1]-$non_repeat->[0])+1;
- }
- }
-
+ foreach my $non_repeat ( @$non_repeats ) {
+ $count += ($non_repeat->[1]-$non_repeat->[0])+1;
+ }
+ }
- print "repeat-> ".$count." are none repeat regions out of $this_block_size\n";
my $percentage_repeat = (($this_block_size-$count)/$this_block_size)*100;
- push @density_features, Bio::EnsEMBL::DensityFeature->new
- (-seq_region => $slice,
- -start => $current_start,
- -end => $current_end,
- -density_type => $density_type,
- -density_value => $percentage_repeat);
+ my $df = Bio::EnsEMBL::DensityFeature->new
+ (-seq_region => $slice,
+ -start => $current_start,
+ -end => $current_end,
+ -density_type => $density_type,
+ -density_value => $percentage_repeat);
+
+ $dfa->store($df);
$current_start = $current_end + 1;
}
-
- $dfa->store(@density_features);
- print STDERR "Created ",scalar @density_features," repeat density features ";
- print STDERR "for ",$slice->seq_region_name(),"\n";
-
-# print_features(\@density_features);
}
}
diff --git a/misc-scripts/density_feature/snp_lite_density.pl b/misc-scripts/density_feature/snp_lite_density.pl
index 48d9e51882..c382c89fd5 100644
--- a/misc-scripts/density_feature/snp_lite_density.pl
+++ b/misc-scripts/density_feature/snp_lite_density.pl
@@ -85,8 +85,6 @@ foreach my $slice (@$top_slices){
$current_start = 1;
- my @density_features=();
-
print "SNP densities for ".$slice->seq_region_name().
" with block size $block_size\n";
@@ -104,14 +102,13 @@ foreach my $slice (@$top_slices){
#
# How many snps fall into this subslice
#
-
foreach my $snp (@{$sub_slice->get_all_SNPs()}){
if( $snp->start >= 1 ) {
- $count++
+ $count++
}
}
- push @density_features, Bio::EnsEMBL::DensityFeature->new
+ my $df = Bio::EnsEMBL::DensityFeature->new
(-seq_region => $slice,
-start => $current_start,
-end => $current_end,
@@ -120,10 +117,8 @@ foreach my $slice (@$top_slices){
$current_start = $current_end + 1;
+ $dfa->store($df);
}
- $dfa->store(@density_features);
- print "Created ", scalar @density_features, " snp density features.\n";
- # print_features(\@density_features);
}
--
GitLab