Now delete old features before starting to avoid creating duplicates.

misc-scripts/density_feature/percent_gc_calc.pl

@@ -64,6 +64,10 @@ my $aa  = $db->get_AnalysisAdaptor();
 my $slices = $slice_adaptor->fetch_all( "toplevel" );
 my @sorted_slices =  sort { $b->seq_region_length() <=> $a->seq_region_length()} @$slices;
 
+print "Deleting old PercentGC features\n";
+$sth = $db->dbc->prepare("DELETE df, dt, a FROM density_feature df, density_type dt, analysis a WHERE a.analysis_id=dt.analysis_id AND dt.density_type_id=df.density_type_id AND a.logic_name='PercentGC'");
+$sth->execute();
+
 
 #
 # Create new analysis object for density calculation.
@@ -131,7 +135,7 @@ foreach my $slice (@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);
 
   }

misc-scripts/density_feature/repeat_coverage_calc.pl

@@ -64,6 +64,13 @@ my $dfa = $db->get_DensityFeatureAdaptor();
 my $dta = $db->get_DensityTypeAdaptor();
 my $aa  = $db->get_AnalysisAdaptor();
 
+#
+# Clean up old features first. Also remove analysis and density type entry as these are recreated.
+#
+
+print "Deleting old PercentageRepeat features\n";
+$sth = $db->dbc->prepare("DELETE df, dt, a FROM density_feature df, density_type dt, analysis a WHERE a.analysis_id=dt.analysis_id AND dt.density_type_id=df.density_type_id AND a.logic_name='PercentageRepeat'");
+$sth->execute();
 
 #
 # Create new analysis object for density calculation.
@@ -144,21 +151,21 @@ foreach my $slice ( @sorted_slices ) {
       }
     }
 
-    #while ( $small_end + $small_blocksize <= $chunk_end ) {
-    #  # here we can do the small sized density features
-    #  $small_start = $small_end+1;
-    #  $small_end += $small_blocksize;
-    #
-    #  $repeat_size = $rr->overlap_size( "1", $small_start, $small_end );
-    #  my $percentage_repeat = $repeat_size / $small_blocksize * 100;
-    #
-    #  push( @dfs, Bio::EnsEMBL::DensityFeature->new
-    #    (-seq_region    => $slice,
-    #     -start         => $small_start,
-    #     -end           => $small_end,
-    #     -density_type  => $small_density_type,
-    #     -density_value => $percentage_repeat));
-    #}
+    while ( $small_end + $small_blocksize <= $chunk_end ) {
+      # here we can do the small sized density features
+      $small_start = $small_end+1;
+      $small_end += $small_blocksize;
+
+      $repeat_size = $rr->overlap_size( "1", $small_start, $small_end );
+      my $percentage_repeat = $repeat_size / $small_blocksize * 100;
+
+      push( @dfs, Bio::EnsEMBL::DensityFeature->new
+        (-seq_region    => $slice,
+         -start         => $small_start,
+         -end           => $small_end,
+         -density_type  => $small_density_type,
+         -density_value => $percentage_repeat));
+    }
 
     if (@dfs) {
       $dfa->store(@dfs);