From ca68357545d137b495a5360199ce5c7ae49b1b17 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Wed, 11 Apr 2012 17:15:18 +0000
Subject: [PATCH] store density features in batch
---
misc-scripts/density_feature/percent_gc_calc.pl | 12 ++++++++++--
1 file changed, 10 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/density_feature/percent_gc_calc.pl b/misc-scripts/density_feature/percent_gc_calc.pl
index 148a125225..7458fa66ed 100644
--- a/misc-scripts/density_feature/percent_gc_calc.pl
+++ b/misc-scripts/density_feature/percent_gc_calc.pl
@@ -136,6 +136,8 @@ my ( $current_start, $current_end, $current );
my $slice_count = 0;
my $block_size;
+my $total_count;
+
while ( my $slice = shift @sorted_slices ){
$block_size = $slice->length() / $bin_count;
@@ -172,14 +174,20 @@ while ( my $slice = shift @sorted_slices ){
-end => $current_end,
-density_type => $density_type,
-density_value => $gc);
- #print join ("\t", $slice, $current_start, $current_end, $density_type, $gc, "\n");
- $dfa->store($df);
+ push(@density_features, $df);
+ if ($gc > 0) {
+ #density features with value = 0 are not stored
+ $total_count++;
+ }
}
+ $dfa->store(@density_features);
+
last if ( $slice_count++ > $max_slices );
}
+print STDOUT "Created $total_count percent gc density features\n";
#
--
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